Okay, so I'm having massive problems keeping net positive cash flow, and checking my economy reveals that I'm paying out a lot of money in starbase taxes, in accordance with a United Planets law.
The law states that an 8 bc tax is to be paid for each starbase in another race's sector.
All of my starbases are in my territory, and they are also in sectors in which I hold at least the majority of the territory. I'm not sure what qualifies the starbases as in enemy territory, but I really can't see how these are.
This is probably a rare bug, because that particular UP law has to be passed for it to even have a chance to occur, but it is crippling - At best I have a 200bc deficit each turn, paying over 600bc in starbase tolls.
Running an AMD 2800+, 1GB RAM, GForce 6600GT with updated drivers, though I'm not sure that helps any.