I just tried yesterday on a brand new (firmware updated) PVT.
Same issue on a home made tape. It really seems that a "glitch" (either tracking or some sort of mangled video signal) triggers a macrovison-like protection (the video is still there but green-ish).
I opened a case at Pinnacle/AVID requesting a patch.
In home made videos can happen that during a stop-start of the video camera (stops between shots) the input video gets "mangled" for a second or two but this shouldn't stop PVT from converting all the remaining footage.
And if is indeed a false positive trigger on a copy protection... damn it, release an updated firmware!