Well I just ran update-fixes 1.2.4 on 5 different machines and all are working properly after the running of the program. The only error I see is that the cdrmysql.tgz file did not download for you. Just checked it and it is fine and all of the other machines successfully downloaded them (BTW the 5 machines are all on different ISP's located all over north america) Try running update-fixes one more time and see if the cdrmysql.tgz downloads. It appears you are having some problems connecting to the internet.
Attached is one of the logfiles I just ran on a system located in Canada on the Shaw commercial backbone for your viewing pleasure.
Problems do occur on some configurations of hardware/software which we cannot predict. I have two intel motherboards exactly the same model and revision of which one will not run PIAF at all. The other is a production server which works flawlessly with PIAF. The one that won't run PIAF will also not run any of the other flavors of asterisk, yet it runs <shudder> XP and Centos 5.1 great. (BTW both of these machines are name brand bought from the same vendor at the same time with exactly the same configurations)
I wish I had an answer however yours is the only report of a system being "bricked" I have had so far. All of the scripts I release are also run on my commercial installs and so far (27+ systems) none have experienced any problems with this update-fixes program similar to yours. Thus I am afraid I have no answers for you at the present. Generally when something like this occurs it is more cost effective to scrub and reinstall PIAF and see if it occurs again. If not then something else is at work if it does then I suspect there may be some type of hardware problem.
BTW since the medium of typed responses is inexact this is not a flame!
Tom
=======================================================
update-fixes - Begin Log 200801151347
Released on Date 011208 Version 1.2.4
=======================================================
<<>> Begin update-fixes ************************************************
<<>> Correcting ARI Mistmatch ************************************************
Now patching /var/www/html/recordings/includes/main.conf.php with localhost|127.0.0.1|
<<>> Correcting format_au error ************************************************
Fixing format_au.so error
`modules.conf' -> `modules.conf.orig'
Patching /etc/asterisk/modules.conf with sed -e '/load => format_au.so/d'
removed `/etc/asterisk/modules.conf.orig'
<<>> Correcting NONE error in service log ************************************************
The /var/lib/asterisk/mohmp3/none folder exists no changes!
<<>> Correcting TTS ownership issue ************************************************
Changing ownership of /var/lib/asterisk/sounds/tts to asterisk:asterisk
ownership of `/var/lib/asterisk/sounds/tts' retained as asterisk:asterisk
<<>> Correcting cdr.conf ************************************************
/etc/asterisk/cdr.conf exists no update
<<>> Correcting festival.conf ************************************************
/etc/asterisk/festival.conf exists no update
<<>> Correcting followme.conf ************************************************
/etc/asterisk/followme.conf exists no update
<<>> Correcting cdr_custom.conf ************************************************
/etc/asterisk/cdr_custom.conf exists no update
<<>> Correcting meetme errors ************************************************
Correcting errors to meetme configuration files
--13:47:35--
http://www.pbxinaflash.org/files/meetmepatch.tgz
Resolving
www.pbxinaflash.org... 216.239.128.70
Connecting to www.pbxinaflash.org|216.239.128.70|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15692 (15K) [application/x-tar]
Saving to: `meetmepatch.tgz'
0K 100% 77.7K=0.2s
13:47:35 (77.7 KB/s) - `meetmepatch.tgz' saved [15692/15692]
File succesfully downloaded. Now extracting file
conf_control.php
manager_custom.conf
phpagi.php
removed `/root/meetmepatch.tgz'
removed `/var/www/html/meetme/conf_control.php'
`/root/conf_control.php' -> `/var/www/html/meetme/conf_control.php'
changed ownership of `/var/www/html/meetme/conf_control.php' to asterisk:asterisk
mode of `/var/www/html/meetme/conf_control.php' retained as 0644 (rw-r--r--)
removed `/var/www/html/meetme/phpagi/phpagi.php'
`/root/phpagi.php' -> `/var/www/html/meetme/phpagi/phpagi.php'
changed ownership of `/var/www/html/meetme/phpagi/phpagi.php' to asterisk:asterisk
mode of `/var/www/html/meetme/phpagi/phpagi.php' retained as 0644 (rw-r--r--)
removed `/etc/asterisk/manager_custom.conf'
`/root/manager_custom.conf' -> `/etc/asterisk/manager_custom.conf'
changed ownership of `/etc/asterisk/manager_custom.conf' to asterisk:asterisk
mode of `/etc/asterisk/manager_custom.conf' changed to 0664 (rw-rw-r--)
<<>> Patching Main web menu ************************************************
--13:47:35--
http://www.pbxinaflash.org/files/menufixes.tgz
Resolving
www.pbxinaflash.org... 216.239.128.70
Connecting to www.pbxinaflash.org|216.239.128.70|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 9549 (9.3K) [application/x-tar]
Saving to: `menufixes.tgz'
0K 100% 108K=0.09s
13:47:36 (108 KB/s) - `menufixes.tgz' saved [9549/9549]
File successfully downloaded
Removing existing /var/www/html/index.php
removed `/var/www/html/index.php'
Removing existing /var/www/html/login.php
removed `/var/www/html/login.php'
Removing existing /var/www/html/favicon.ico
removed `/var/www/html/favicon.ico'
Now extracting menufixes.tgz
favicon.ico
index.php
login.php
removed `/var/www/html/menufixes.tgz'
Setting permissions and ownership
changed ownership of `/var/www/html/index.php' to asterisk:asterisk
changed ownership of `/var/www/html/login.php' to asterisk:asterisk
changed ownership of `/var/www/html/favicon.ico' to asterisk:asterisk
mode of `/var/www/html/index.php' retained as 0766 (rwxrw-rw-)
mode of `/var/www/html/login.php' retained as 0766 (rwxrw-rw-)
Stopping httpd: [60G[[0;32m OK [0;39m]
Starting httpd: [60G[[0;32m OK [0;39m]
<<>> Now patching configedit ************************************************
Now patching cls_phpconfig.php
--13:47:36--
http://www.pbxinaflash.org/files/configedit_patch.tgz
Resolving
www.pbxinaflash.org... 216.239.128.70
Connecting to www.pbxinaflash.org|216.239.128.70|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3638 (3.6K) [application/x-tar]
Saving to: `configedit_patch.tgz'
0K 100% 1.27M=0.003s
13:47:37 (1.27 MB/s) - `configedit_patch.tgz' saved [3638/3638]
File
http://www.pbxinaflash.org/files/configedit_patch.tgz downloaded successfully
`/var/www/html/maint/configedit/cls_phpconfig.php' -> `/var/www/html/maint/configedit/cls_phpconfig.orig.php'
cls_phpconfig.php
removed `/var/www/html/maint/configedit/configedit_patch.tgz'
<<>> Now patching freepbx ************************************************
Patching FreePBX security hole in /etc/httpd/conf/httpd.conf with Patch A
<<>> Now fixing error with CDR not working after update-source run ************************************************
--13:47:37--
http://www.pbxinaflash.org/files/cdrmysql.tgz
Resolving
www.pbxinaflash.org... 216.239.128.70
Connecting to www.pbxinaflash.org|216.239.128.70|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 518 [application/x-tar]
Saving to: `cdrmysql.tgz'
0K 100% 42.3M=0s
13:47:38 (42.3 MB/s) - `cdrmysql.tgz' saved [518/518]
File
http://www.pbxinaflash.org/files/cdrmysql.tgz downloaded successfully
Moving original file to /etc/asterisk/cdr_mysql.conf.org
`/etc/asterisk/cdr_mysql.conf' -> `/etc/asterisk/cdr_mysql.conf.org'
Now installing new cdr_mysql.conf file
cdr_mysql.conf
removed `/etc/asterisk/cdrmysql.tgz'
changed ownership of `/etc/asterisk/cdr_mysql.conf' to asterisk:asterisk
mode of `/etc/asterisk/cdr_mysql.conf' changed to 0664 (rw-rw-r--)
<<>> Now fixing recodings not being saved error ************************************************
Now fixing permission and file errors when saving voicemail or custom greetings
<<>> Now fixing some miscellaneous errors in httpd log ************************************************
Patch 119 has already been installed!
<<>> Now applying patch 120 ************************************************
Patch #120 now applied
<<>> Now applying patch 121 ************************************************
Patch #121 rewritten /var/www/html/index.php installed
<<>> Now applying patch 122 ************************************************
Patch #122 fixed http error on port 9080 applied
<<>> Now applying patch 123 ************************************************
Patch #123 internal program errors and enhanced logging applied
<<>> Now restarting asterisk ************************************************
STOPPING ASTERISK
Disconnected from Asterisk server
Asterisk Stopped
STOPPING FOP SERVER
FOP Server Stopped
SETTING FILE PERMISSIONS
Permissions OK
STARTING ASTERISK
Asterisk Started
STARTING FOP SERVER
FOP Server Started
<<>> End update-fixes ************************************************
=======================================================
update-fixes - Finished Log 200801151347
=======================================================