Strange this should work flawlessly. I use parallelprocessing to start comskip and postprocessing for other tasks.
Is it possible that another process started in postprocessing is doing something causing comskip to fail?
I am not sure whether there is a difference between starting comskip in parallelprocessing and from within GBPVR in terms of starting postprocessing. when run from parallelprocessing postprocessing only starts when parallel is finished. When comskip runs from within GBPVR I am not sure. Maybe this is your problem?
AMD 780G with X2 BE2350, 2gb ram, LCD-TV, Win XP
PVR500, PVR150 & PVC150 MCE MediaMVP D3A, 2 networked clients