I first set it up in Nov or late Oct and the black frames only became an issue in the last week or two. During that time I've upgraded VM to 98E/F and played around with stacking etc. During the stacking and/or(?) averaging trials, pics would be stored on the card (according to the cam test routine after a crash) and at times, depending on what I had the cam's native resolution set to, would only report room for 6 frames! During that setup, it would definitely crash during stacking. Reformatting the card would clear it but frames would later be reported on the card again. Thinking back, I can't remember if just pulling the USB cable w/out a format did anything.
I'll have to do a cam preview next time it crashes or black frames and see what's on the card - something ends up on it to the tune of 5 or 6 frames the one time I checked during image stacking crashes. I would think if VM is not utilizing the card at all, there shouldn't be any change in the card's contents - unless it pipes thru the card and leaves residual crap after a crash; not being able to clean up after itself.
Clearing the OS buffers does makes sense except for the 7 or 8 months of clean operation. Perhaps a quirk in 98E/F? I was using 91D prior to May 21st and started playing with the stacking/averaging around the 24th for a few days.
Maybe the card is failing - I've heard they had a reputation for that in the past.
What version VM were you running during your black frames?
Did you get them with the 765 and its xD mem card?