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I don't know how comfortable you are poking into your case but, I would suggest opening your case and checking to make sure that the ide cables are plugged in properly, i tsounds like they might be loose and after your computer has warmed up, the connection is just "off" enough to stop detecting your drives during the install. Other then that also check the master/slave jumpers on both drives.
I do not recommend playing with the jumpers if you aren't comfortable opening your case, but just pushing cables back into the connectors should be somewhat easy (but be warned that there are lots of cables).
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