I believe this has been addressed, or at least is being looked into. From what I've heard/noticed, any games submitted with v1.2 b1 using a non-custom race were flagged with cheating. I had the same problem when playing as the Drath.
My guess is that it's caused by negative ability points that aren't detected until after you start the game (Assuming you modify the pre-defined race some) As the Drath, I was essentially getting a free +50% to defense since their wasn't a racial ability for +50% defense, just 10, 20, or 30.
Therefore, every predefined racial ability that didn't match a bonus exactly with a selectable one was given for free, and any remaining points that would've probably been used for it are free. So when those are used, you will see a '0' in points remaining after, but the game may subtract the points from the "freebie" attributes thus producing a negative number that we can't see.
That is only my theory, but as for fixing it, send a saved game to
[email protected] and explain what's wrong.