I haven't looked at the SVN logs because I haven't had time yet, Sushi, but if you'd like to take a look, the problem was reported to appear between RCs 3 and 4. Here's the thread:
http://www.hard-light.net/forums/index.php?topic=80273.0Zookeeper, FSO additions (both features and fixes) that have any potential to change balance or AI should always be off by default. The problem is that we usually
don't know whether gameplay is going to be affected, and nobody has time to play through every single released FreeSpace mission to be absolutely sure. Yes, it's annoying, but what is even more annoying is when FSPort or Blue Planet mysteriously becomes unwinnable and nobody has any idea what happened. (See the thread linked above.) Then people have to go and either comb through the code or carefully compile and test builds for each SVN revision.
So this is a policy born of necessity. We want to save ourselves an awful lot of frustration and lost time down the road.