One further suggestion -- are the data files on a remotely mounted disk, versus a local disk? That can cause trouble for 3dGroupInCorr due to the way it loads the .data file -- it "memory maps" it rather than "reading" it. But some remote disk mounting solutions don't work well with "memory mapping" I/O, and so may (silently) give nothing.
I thought of this, since looking at the 3dSetupGroupInCorr.c code, it checks the each input dataset to make sure it isn't all zero, and will complain if that happens -- and you would have noticed the error messages.