Any drive in Bay 2 freezes MacPro 1.1

I have a 2006 MacPro that has given me trouble free performance since I bought it. I'm way over due for a new system. I'm holding out for the release of the new MacPro.
Anyway, during the past week or so my system was unstable. First - I couldn't get it to wake from sleep without rebooting. A few nights ago I returned to my work area after about 5 hours and took it out of sleep mode. When it started up there was a warning message on the screen stating the the internal HD installed in Bay 2 was improperly ejected. I didn't think it was the drive since it was fairly new and has had light use. I did go ahead and replace it with a brand new drive.
System started up fine. I formatted the new drive, and everything worked as expected. A few hours later the system became unstable, eventually locking up. When I tried to reboot - nothing except a gray screen. I tried booting off CD and a bootable Lion USB Flash Drive. No luck with this. No options to select boot drive ... nothing. Just a gray screen.
Well the system is back up and running. It turns out that if any drive in inserted in Bay 2 - it's impossible to boot. Once I remove the inserted drive, the system reverts back to normal. Definitely not the drives. They've been tested externally and are 100% fine.
Is there anything that I can do to fix this? Sounds like a bad HD controller on the logic board. I don't plan on getting it serviced due to it's age and my eventual purchase of the new MacPro.
thx.
-paul

The hatter wrote:
Did you ever do a "hot swap" with a drive in that bay? some "get away" but it can damage the electronics.
Your running Lion, at some point have you already started over with a clean install? not upgrade over SL?
One way to work around only having 3 drive bays are the two ODD ports, and two SSDs (not bootable) on Sonnet Tempo SSD PCIe card.
Just what type make model of hard drive did you buy that you are trying to use?
Thanks for the tips ...
Never hot swapped. The system was always powered down and unplugged when necessary. And no, I've never done a clean OS install on this system. Like I said, it's been trouble free since I bought it. I mostly run media production applications. I'm going to consider doing a clean install.
As far as the drives that I use - these Western Digitals
The suspect drive that was in Bay 2 works fine when I use it in a docking station. I also tried 2 brand new drives in Bay 2. The problem persists. As soon as I remove the Bay 2 drive, the system boots and works fine.
The ODD/SSD option is cool. OTOH I'm basically holding out for the new MacPro. I'd still like to solve this Bay 2 issue before I decommission the system or sell it, potentially.
-paul.

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*Apologies in advance for the lengthy post. I just want to be sure I include as much detail as possible. Thanks in advance for reading all of this and offering any thoughts and suggestions.
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