Stratguy,
I know this is an old post of yours but I just saw it and thought I would reply. This sounds like a clock source issue you are having. If I am not mistaken, when using the SPDIF input on the VM3100 Pro, you have to set the VM3100 Pro as a slave and the connecting device such as your GT-Pro as the master clock source. You may also need to adjust your DAW software accordingly but I do believe that should solve your problem.
Best of luck.
I am using the VM3100, RPC-1 and I have a Johnson J-Station that I used the SPDIF on when I first purchased but due to having to alter the clock source settings, I just used the 1/4 outs and honestly my ears don't reallly hear the difference. I hate to get bogged down with too much technical stuff when I am trying to create music so that was an executive decision!