Try adding the default color effect onto any clips which have copyguard.
This solved a similar problem for me recently when trying to output a timeline via firewire into a dsr-45. That same dsr45 was initially used to record that short sample of copyguarded footage from dvd (via s-video). During transfer, the dsr45 presented warnings, yet the footage looping thru the dsr-45 and into avid via firewire, captured nicely into the avid and looked fine in the Composer window/Timeline– as was well until I tried a digital cut.
A videwomixdown didn’t work– so I used a color effect and was successful.