Alverin, you're right, if it's happening frequently it's not a freighter/trade issue, they don't move that fast. But I have noted that the Research screen 'turns left' doesn't update itself properly (easy way to see this is to start the game with +70 research, you'll still see a '16 turns to go' for each tech just as if you had +0 research). Perhaps that is causing you problems when you adjust your sliders?
Another thing that might do it is GalCiv's often strange (at least to me

) model. To see what I mean, grab your research slider and move it from 100% to 0% and back and watch your income go way up and way down as you do. Possibly this is causing your problem as well, by moving the slider the turn before a project finishes you are basically changing you economy around, and combine that with the 'turns to go' not updating properly...
I never microed my research in GalCiv (I have in other 4x games), so that is probably why I've never seen this happen.