are you referring to this http://www.youtube.com/watch?v=f1D_UurOook?

I would suggest you to use CUE or MASTER track as sampling sourc SRC3 and not the MAIN…for the aforementioned issues.

i am trying to sample a THRU machine and listening at the same time the recorded audio.
Having the crossfader in middle introduces really tiny subtle phase issues…but this is fair enough.

Can you better check your Scenes? maybe some other parameters got locked without you being aware of this.