Mac Pro requires repeated attempts to boot up correctly

I have a late 2007 quad core Mac Pro (2.66GHz) which is about 14 months old. Over the last month I have started having problems booting up.
Initially pixelated patterns started appearing over the desktop and the dock and pretty soon the screen would just start flashing. Now it generally takes 4/5 attempts to boot up correctly with the first 2 attempts not doing anything after the startup chime.
I have tried booting up without external hard drives plugged in, I have reset the PRAM, tried booting in safe mode and I have done an archive and reinstall all with no joy
According to the Apple hardware test everything is fin. Disk utility says there are no problems with the hard drives. The only issue are permissions... I have repaired permissions but immediately after doing so there are more issues with permissions. I have heard mention of problems with a software update for the NVIDIA GeForce 7300 GT card I am using but when I had the same problem when I loaded the older version of the OS during the archive and reinstall.
Any help would be greatly appreciated. Incidentally once the computer is up and running it works fine.

First, don't rely on Apple Disk First Aid to tell you if everything is fine or not, or to repair problems.
Make sure you have two bootable systems, 3 would be preferable.
Invest in SuperDuper, some backup drives, and then Disk Warrior or something. Then run those and do more as far as preventative maintenance.
There was a firmware update a long time ago for the 7300GT. Software updates are not going to cause problems. The card may need to be replaced and hardware failure, but take that up with your AppleCare.
If your external drives are bootable, pull your normal boot drive and try with those.
NEVER repair permissions except with the latest version of OS X you run (10.5.6).

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