I doubt very much it's a compatibility issue - when you export to tape you're just doing exactly that: recording to tape. I may be wrong here, but I don't think you've done anything differently by using a different application.
Then again, I've been wrong before and I'll be wrong again! I just really think it's the fact that your client's hard disks are in a bad way - check out past posts to see the amount of times dropped frames have been due to a badly fragmented drive!
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