I never knew SF could do multitracking... can it? or is this new with 6.0? I've been using 5.0 for a while now for editing and mastering, and never noticed anything like that...
I actually just use Fruity loops for the creation of loops; usually just drums, but every once in a while i'll do some stratch key pads with it (i don't use synths on finished recodings; i multitrack and process the heck out of direct-recorded guitars to get the same effect, it's more fun.

) I then use Acid to assemble backings. I find this is the most flexible solution for me...
-Drew