I'm not much for looping audio, and usually work in Logic...

I've heard a lot of good things about the Soundforge/ReCycle combo. Soundforge doesn't have very many tools specifically for adjusting the "groove" of a loop (sure, it *can* do it, but you have to know exactly how first). I would suggest maybe using Soundforge to master and EQ your loops first, get them sounding the way you want, then throw them into ReCycle for editing the groove, shuffling bits around, etc.

I've only used an older version of FL, but I don't remember there being many tools for audio loop editing. I'm very likely wrong though.