Just to offer one more update, I may have confirmed that this issue is
somehow related to the the 3ware driver. I removed the 9690 card and
replaced the 9500 8 port with a 9500 12 port and a seperate LSI (still
PCI-Express) card for the external array and did a fresh install of
Debian 4.0r3. The installation went flawlessly and was up and running
in no time. I then replaced the LSI PCI-E with an LSI PCI-X and the
system booted painlessly again.
Again I think it may be related to the module rather than the card
it's self because when we moved the boot drive that was loading a 9690
module to a system without a 9690 (but did have a 9500) we still saw
the same error. The 4.0r3 install also worked fine until we upgraded
the kernel in order to see the 9690 card. After that upgrade was when
we started seeing the slow to respond issues.
As a final check I decided to boot one of the backport images that has
2.6.25 kernel and I get the same error so it seems that this is
related to the newer version of the 3w-9xxx (or possible the 3w-xxxx)
module. The version that is in 2.6.18-6 works fine but 2.6.25 results
in errors on our SSD drive.
Hopefully this information is helpful in clueing someone in to what
the problem may be. As for us we're going to be running 2.6.18 for a
while it looks
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