Do you have basic working experience with that specific setup? If so, assuming that you have more than those two extensions, and some of them work well, compare their settings (outbound route settings for an extension that works well vs fails).
Those two faulty extensions, can they dial other extensions?
You've mentioned that as the biggest issue. What else is wrong? Maybe they are related. The more info you provide the more help you would get.
If you have no practical experience with this platform not only you would need to catch on with the reading material, but you would also need a test platform to experiment. Just make sure that you don't create new problems inadvertently on the current one. The software being an old version I am not sure you can still find it for a fresh new install, but you can probably replicate your existing machine, even virtualize it, so that you can use it as a test platform.
If the current system is not critical and you can wipe it for a new setup, then go for the latest version and start fresh. It's really quite simple to get a PBX running with basic functionality. Just make sure that you have all your trunk info and call routing rules properly saved from your current system (including paper copy) so that you can enter it in your new one.