Dear Daniel and Nick,
I agree with Daniel in that it would not be very difficult to create this function since it is basically shuffling the phase of the FFT of the voxel time series, and then apply the inverse FFT. Meanwhile, I've created my own 3dFFTshuffle using the R interface to create AFNI compatible programs, as described in 3dRprogDemo. Please contact me (c.caballero@bcbl.eu) so that I can share them to you. If anyone else is interested, I could upload them in the distrubution but my feeling is that an implementation in C will be much faster and not difficult to do.
Best,
Cesar