I’m no help here, but we experience the same thing at our shop. It happens for us with DSLR footage all the time (transcoded or not). As best we can tell it corresponds to the time code in the file, how PP reads it, and how PP interprets it upon XML export.
Our common problem lies in going from PP to DaVinci Resolve. The cuts come into Resolve nowhere even close to what the PP timeline actually shows. My only guess is that PP is having problems dealing with the timecode/metadata of the file. I never had this issue with FCP7.
Glad to know we’re not alone over here….sorry I’m not more help.
Ryan