Hi Mark.
Correct me if I'm wrong, but doesn't the empeg software rely on the scratch partition to be at least 16MB in size? And AFAIR the same is true for the software partition. You could of course tweak the kernel to redirect any access to the scratch partition to actually access the appropriate partition on the second HD, but I think that would defeat most of the benefits of using a CF as the first HD, wouldn't it?
cu,
Sven
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proud owner of MkII 40GB & MkIIa 60GB both lit by God and HiJacked by Lord