Not sure this qualifies as a "common" problem. I don't recall reading a mass of posts about it.
Out of curiosity, what kind of media are the clips?
We have had issues opening CS3 Projects in Premiere CS4. You're better off keeping a copy of Premiere CS3 on a computer for situations where you need to do revisit these projects. I believe that Adobe changed/corrected the video aspect ratio in CS4 and the programming "math" gives CS4 a fit when you try to edit CS3 prproj's. If you have a single full quality file exported from the old CS3 project (for instance DV NTSC), if practical bring that single chunk of video into a new CS4 project and make the changes to that.
I've seen something similar. Occasionally, we'll capture a tape in CS4 and the clip plays back at hyper speed while the audio stays at normal speed. It usually hangs on the last frame of the video. The work around has been to save, close Premiere, and re-open. After that, it's fine.
the programming "math" gives CS4 a fit when you try to edit CS3 prproj's
I did not have any such problems myself with converting either CS3 or 2.0 projects.