CS5 keeps losing prefs

Question

I am pretty sure by now that there are some performance issues with CS5 on my system.
First I thought it was random that my brush tools cursors occasionally become the hand or move tool, and I can't get the brush back most times. I also notice that when this happens my background mode colors keep going back to default grey or blue. I always set my BG colors to black, and after weird stuff happens, they go back to default.
I also get tons of "Photoshop quit unexpectedly" dialogues after saving and closing files, or simply quitting the program.
Sometimes, saves will take tons of time, or freeze up with spinning ball for 4-5 minutes on normal files.
Brushing with paintbrushes are slow, even with respect to the perhaps poor Wacom drivers or nvidia drivers...
Other things are simply not performing well, it is not all coincidence anymore. I can't be sure that all this 64 bit stuff made all that much difference, Maybe I saved 5 minutes per day of processing? It is not worth it.
I have cleared cache, rarely even use fonts, but I cleaned that up as well, system is kept clean... there is no reason I should be having these sort of problems. We upgraded to SL, bought CS5 and bought more RAM for better 64 performance. This stuff cost lots of money, and probably compromised a few co-workers bonus or raises here. Unfortunately none of the upgrading has been worth it as of today, and I can't go to my boss and tell him that Photoshop isn't working, all he knows is that the owner approved these upgrades, to them it is a ton of money and an investment that my work will speed up, and my system will operate as I said it would.
sorry for the rant.

Answer 1

Specifics.
Mac Pro Quad 2 X 2.26
Nvidia GT 120 card.
OS 10.6.4
Photoshop 12.0.1x64
364 GB left on disk
using a Western Digital USB drive for scratch disk (and Time Capsule backup) it has 406.36 left
8GB RAM
Photoshop uses 86% (6509MB of ram)
Cache levels = 5
Tile size 1024
Open GL is on advanced
No additional plug-ins used in Photoshop.
File sizes are ~200 - 500MB tiffs generally, no fonts being used in Photoshop, 4-5 layers mostly adjustment layers, nothing special.
I am able to get the work done, it's not freezing while working or anything, it's just that I can tell that it is not performing as it should. Hard to explain, but these glitches are happening too much, and sometimes slowing down during small projects... it is not right. Computer is very clean, I always keep my equipment (software/OS) clean.