Hmmm. When you installed the second disk, did you use Empeg's disk formatter upgrade file to initialize it? Or did you try to partition it yourself? If the latter, then that could be the reason. It's possible there's something it doesn't like about the way you hand-formatted the drive.
Also, are you running the latest player/emplode software (1.02 at this writing)? Certain earlier builds were reported to have problems during synch that would cause them to take too long to do a disk check.
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Tony Fabris