Dear functional conn comunity, 

I have been wondering the same thing. Denoising seems to shift the distributions towards having mean 0 (although in most cases there is a longer tail on the positive side).  This will induce "spurious" negative correlations as well as somewhat change the output of weighted graph theory measures i imagine.
I am not sure what part of the denosing may produce this (e.g., simple movement within the scanner may produce higher correlations). I might investigate myself if I find time; but in the mean time any comment or discussion is welcome. 

Happy connectivity
Peter