Mac Pro with Lion 10.3 'forgets' its optical drives

I've got a really weird problem here, and I think that I can discount a hardware fault since this problem manifests on two Mac Pros (a 2009 Octo-core and a 2009 Quad-core).  When I start either of these machines up with Snow Leopard, theres no problem - however, if I boot up using Lion 10.7.3 then both machines suddenly develop a strange problem with their optical drives (both are kitted out with a Blu-Ray writer in addition to the standard Superdrive).
After either machine has been turned on for a period of time (about 30 minutes), they 'forget' that they have optical drives fitted. Up to that point, everything works fine.  After that point, problems occur. When the problem manifests, disk utility hangs when launching. Shutting down the computer entirely, waiting a moment, and then restarting fixes the problem. Merely selecting restart results in the 'No Entry' ( / ) and a failed boot. The problem isn't unique to disk utility - it applies to any program which attempts to access the optical drive. Finder, the eject Menulet, Handbrake, anything. Forcing quit and then restarting is no good either - once an app attempts to access the drive that app cannot be used again after a shutdown and restart, although all other apps running keep running fine.
I have investigated this problem by resetting PRAM, resetting SMU, and ensuring that the latest firmware patches have been applied. None of these worked. I then reinstalled Lion from scratch (erasing the disks first, and clean installing from Lion on a USB stick). Still no luck.
The common factor with both machines is the hard disk (the octo has Snow Leopard, the quad has Lion) - as part of my diagnostics, I swapped the start disks over.  In fact, both machines will run fine with both hard drives installed - as long as the boot disk is Snow Leopard.
Is this a known fault with 10.7.3?  Has anyone else experienced this?  Or is it, as I suspect, a duff hard disk?  Mind you, if it is a duff hard disk, how come it doesn't cause problem except when it's used as a boot disk?

These sorts of problems are often caused by peripherals that do not tolerate [√] put the hard drives to sleep when possible, or Deep Sleep.
They can be solved by not sleeping, and there are also some very complex ways to disable deep sleep that you can search for is you want to bad enough.

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