Hmm, well I did not have my CD-ROM cable plugged in fully, that's why it was booting off the hard drive with ZERO problems.
So I adjusted it. Turned on The CD-ROM, turned on the Amiga, then watched the screen as it sat forever in blackness.
I then Turned off the CD-ROM, booted the Amiga, same thing.
I then unplugged my CD-ROM, turned on the Amiga, now it does not detect a Hard Drive what so ever!!!!
I'm going broke FAST, if my freaking Amiga's IDE port just blew out, I'm going to be pissed!
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EDIT
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Plugged in external 12Gb HD, along with 1. 7Gb internal.
Now it detects the HD again, at least the HD light lights up. But HDTools sees them not. So I unplugged the external HD, rebooted my Amiga, and now the single HD funtions once more.
So does this mean HD Tools could not see them because it does not support modern 6+Gb HD's?