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You may just be dealing with a master/slave misconfiguration. Some HD's require different settings if they're master single or master with slave and they will behave very poorly if the drive connections no longer match the jumpers. Having one drive connected but powered off can do this.
If you can't make heads or tails of what it wants then let us know the brands and models of drives, the arrangement of HD's and opticals on the IDE cables, and the current jumper positions.
i.e.:
IDE1, black (end) = WD model WD800BB 60GB jumpered as master w/slave present
IDE1, grey (middle) = WD model WD2500JB 250GB jumpered as slave
IDE2, black (end) = blah blah DVD as master
IDe2, grey (middle) = blah bah CDRW as slave
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