The Terran AI decided to be nice to me when he lost and gave me all his assets. Wow thanks right?, nope. He was in dept and i ended up with -1400 in balance. My strategies involved to only have money to pay for maintenance so when this hit me I lost the game. Had to wait a lot of turns to get my balance over 0. And when it did the noting resumed. I Could not produce anything nor research. Gee, thanks for that gift... next time die in silence.
Don't let AI give negative balance. And try to resume production if that's the system you want for being in dept...
I'm going back to master of orion 2...
the governance sliders don't always move back to their default position.
I filed a bug report to this, and it seems, to me at least, is that if I change the default position of the sliders (say, more economy than research) before going bankrupt, the sliders never come back to normal once I'm in the black.
When an AI surrenders to me, I first look at their colonies to improve them, then I check their ships. They are usally way lower tech than mines, so I destroy them, along with any stranded shipyards, that saves some money/turn and it speeds up your economic recovery 
As for the negative balance immediatly after the transer, it might be a bug, so as others said, file a bug report.