To follow up, I decided to e-mail Canopus technical support on the off chance this is a Premiere Pro plugin issue (I own the the DV Storm 2 Pro). Here is the reply I just received (I haven't tried the workaround yet):
That is a feature that we do not support in Premiere Pro for the fact that it works sometimes but not all of the time, and we haven't been able to trace back in the Adobe SDK what causes it. The workaround is to change the project settings to standard Premiere settings (no Canopus presets), then adjust the timecode on the DV files, and finally bring it back into the original project.
If you have any other questions please let me know.