First of all, this problem happens only on Armada 1. On 2, I never have a problem. This also happens on all my computers, including one that has 3 GB of RAM, though not as often on that one.
Anyway, to fix this problem, I've simply replaced the borg transwarp gate with a building that, when built, gives all Borg ships the ability to transwarp using a different version of the Interceptor's Transwarp weapon. My friends and I agree that this makes the game more challenging, because there is no warning when several Borg fleets simply appear in an area. All I need now is some sort of special weapon that causes shroud to regrow in a certain area, as a means for another race to counter this ability.
All of my questions are for Armada 1!