Rakeback comes out of MGR. MGR is basically how much rake you've generated on Full Tilt.

There are lots of things that can reduce your MGR. Bonuses is one of them. Playing in tournaments with overlay or buying stuff from the Full Tilt store will also reduce your MGR.

So yeah, clearing that bonus is reducing your rakeback. But that's not a bad thing. You're making more money than you would with full 27% rakeback and no bonus. Technically you're making something like 50% rakeback.