[Suicide Junkie]

The way to confirm it would be to:
1) attack an undefended homeworld with a brand-new transport. Count how many militia survive.

2) reload the game, and use the same troops on an experienced transport. Count how many militia survive this time.

Be sure to repeat steps 1 and 2 a few times to smooth out the randomness inherent in combat. If you still see a significant change in the results of combat, then the experience may be the cause.