I've been using my FCB with Guitar Rig since GR2, so I do know of what I speak. I have NOT upgraded to GR6 from GR5, but they didn't change anything significant, just added a couple of new amps shot with newer modeling methods.
The problem chrisw_63 referred to only occurs when using an underpowered, un-optimized computer with too low a sample rate.
What are the specs on your computer?
It does NOT sound like the problem you are describing, but without a sound sample it's impossible to be sure.
I strongly advise against using ASIO4ALL, the stock ASIO driver provided by NI works fine.
Record a sample of the noise and attach it, along with a description of the effects in use in the preset. I'll try to duplicate it and look for the problem.