Mac Pro 2006 tower, not showing gray startup screen - "asleep" till desktop appears

Mac Pro 1,1 Dual-Core Intel Xenon, 2.66 GHz, 5GB ram, 2 internal HDs of 500GB and 1T. OS 10.6.8
I suddenly "lost" the normal gray startup screen on my Mac a few months back. I get just a black monitor screen until the desktop appears. I'm having other issues too and want to run disk utility off an external HD to fix internal HD permissions. But when I hold the option key and start, I can't select the external as a startup disk without a startup screen. Any ideas?
I'm wondering if adding the second internal HD may be the cause of this and other apparent memory issues (slower performance, web pages slow or not loading in all browsers, Finder folders only opening after a "wakeup" wait). They seemed to happen around that time, though I can't say I notice an immediate change. Could simply adding more HD real estate be the issue? Thoughts on that too?
I've tried the using Disk Utility before but can't recall if I ever got it to work on the 1T HD due to that lack of a startup screen. I've also played with plug-ins/extensions in browsers and can't say they're to blame.

We have a 2.66 MacPro 1,1 still running fine at present, the original graphics card was replaced by Apple as part of a known issue. This was over 4 years ago, close to the end of the cutoff period for the known issue IIRC.
I'd suggest you contact Apple & see if you can sweet talk them into doing something about the graphics card, even if it's just arranging a better price on a replacement. I recollect at the time of the exchange Apple was switching cards based on the installed OS. Having 10.6 installed meant we got a NVIDIA 8800GT, earlier OS's meant other cards were offered instead. I think it came with a NVIDIA GeForce 7300 GT (but I could be wrong - ask me to dig out details if you want to know for sure).
P.S.
Assuming the disk doesn't contain your user data, shutdown & remove your second HD to see if it runs any better, I find that the OS will wait for what feels like a lifetime when requesting data from a disk that has gone to sleep. SSD's change your perception, booting from one will freshen up the Mac, but won't fix the no graphics at boot issue, sorry.

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