Upon restart system folder can not be found

No problems with machine since last Oct. when I had to replace a stick of ram.
Run down of what has been happening now:
Last week - machine was up and running. Went to start Mail (had it open earlier in day) and got spinning ball of death. Could not force quit. Upon restart system folder could not be found. Restarted again, started up fine.
Yesterday - went to log on in log in screen and once again spinning ball. Upon restart could not find system folder. This time had to restart 4 times and after cutting power and restarting then system folder was found.
I have repaired premissions, verified disk (ok), ran scripts, made sure software was updated, made sure right startup disk was selected. Found 1 bad font, removed this, re-ran everything, rechecked fonts. CS3/safari/mail seem to be running fine. Although I have not done a lot with them as I'm slow with work this week. Hard drive does not sound like it's making any extra noise. Thought this problem might be fixed. As machine was fine this a.m. shut down machine about an hour ago thinking I wasn't going to use for a day, remembered I had to do something and upon restart again, no system folder. Had to cut power again and then starts up. What could be going on?
Any suggestions? Ideas?
Thanks in advance.

Disk utility shows disk being verified & ok.
One thing I didn't think of was resetting the PRAM.... which I found this advice under: Recent User Contributed Tips: a brody - Myths of required versus not required maintenance for Mac OS X (Oct 30, 2008)
3. Repairing the directory. Partially false. Only required if your data is backed up, and access to your files suddenly is limited even after Spotlight indexing is complete. More true if you get a flashing ? disk, though zapping the PRAM sometimes fixes this issue as well.
after doing this so far no problems.

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