I had rather given up trying to find a solution. I’m currently running two different systems one with CS3 for projects already in progress and one in CS4 for entirely new projects.
However, I have ascertained that CS4 actually alters some of the original files. I seem to remember the file sizes of some WAVs changed. I noticed this when comparing folders. I had opened identical projects in CS3 and CS4 – each with its own independent set of identical rushes – after indexing and conforming some of the file sizes had changed. The difference wasn’t much but they had changed.
Sorry, I don’t have anything helpful to say about a solution or workaround but if this extra info helps anybody to debug this nuisance problem then please post back with the fix.