Well the reason I mentioned calling support is because perhaps they can figure out a way to get these files working with the new video improvements. I'm assuming these are files created from BEFORE the patch, right? Kind of like how we have problems sometimes getting older projects to work in the latest version of Sonar (which is why I just finish what I'm working on in whatever version it was created in before moving on). They may know a way of reimporting the video so you can take advantage of the improvements.
I'm not a video guy (yet) but I'm quite happy they took the time to work on this stuff because there are a LOT of old vids I want to sync to audio or simply remaster the audio on and from all I've read I was probably going to have to purchase a separate editor to make it happen smoothly.
Another solution if you have not incorporated many of the new effects that came with X3 into your project is maybe trying to open the project in X2 or X1 which AFAIK have the same video elements of the pre "d" versions of X3 and doing your work there. That way you don't have to rollback or reinstall to finish what you are doing.
Have you tried starting a new video project with X3d? Does it cause the same problems?
After rereading your followup I'm not sure... because as I said I'm not a video guy. It seems perhaps you have tried loading it into a new project. So if that is the case and it is not working then perhaps there is a file format issue that maybe Cake will be aware of.
User gswitz did some tests a couple weeks ago but I didn't fully read those threads. Perhaps do a google search and they'll provide some more insight.
Sorry... not really a video guy. Good luck.