Here's a Doozy!

I'm still in OS 10.6 on an early 2009 Mac Pro with all bays full--4 internal drives, the last partially formatted FAT for use with Windows XP in Bootcamp.

All was fine, worked perfectly, etc., etc. A while back I plugged in a WD My Passport external drive to do some back up. I just kinda left it plugged in (FW800) not paying too much attention to it except when I needed to back up.

One day I got a message asking what I wanted to do about a drive that couldn't be recognized: initialize, ignore or eject. After a few days of ignoring it, I discovered that the drive in the last bay, a large 2TB Green Caviar had ceased to appear in Finder. I put two and two together and at least realized why I was getting that message every time on start up.

In the meantime, I'd unplugged the external drive. What I have learned is that the drive in bay 4 IS recognized, but ONLY IF the external My Passport is plugged in!! How weird is that?

If I unplug the external drive (ejecting it first, of course) and then reboot, again the drive in bay 4 disappears and I get the message that it can't be read.

Does anyone have any idea how it is that a drive in an internal bay can only be seen if/when an external drive is plugged in?

For what it's worth, I can see the drive in both Disk Utility in Mac and Disk Management in Windows, where the drive shows as unallocated space. There's also a notice in Windows Event Viewer that there's a IRQ problem, which is probably a tip as to what's going wrong, though I don't know what to do about it, nor does Microsoft, naturally. The problem might be a Windows problem that's also affecting Mac. The trouble with using Bootcamp in conjunction with multiple drives is that who knows how Windows allocates drive letters, particularly when an external drive is plugged in and then removed. Could the problem be the small portion of the drive I formatted as FAT32 in Windows? Drive Genius seemed to be saying as much, but couldn't be more specific than that, presumably because it works only in Max OS and not in Windows.

Thanks for any help or ideas anyone might have about this. By the way, all the data in the 4th bay drive is fine, though I have copied all of it off thinking I'll probably have to reformat it.