How to fix a looping desktop NOT related to Stuffit?

Question

This very similar to another thread but I feel it's NOT related to it.
At first I thought it was related until I got further into the solution. I did download the 2008-08 security update as well as QT 7.6. That's when I think the problem started. The difference being that after xx iterations, the desk top would appear and work OK. If the computer sat idle for 3 - 4 hours (not likely due to our work load) it would loop again once I woke it up. It always happens sitting overnight. The problem is now approaching 2 weeks of acting this way. I didn't have any of the other symptoms like folder closing, applications quitting, etc.
I thought after looking for this AVR file I realized that I don't have Stuffit anywhere in my system. So that fix would not do me any good. I surmised that it might be a start up item in system preferences under users so I started bypassing them one at a time until I only had one left. That one was bypassed last night and made the loop count the highest ever at 84. Today, I noticed after removing (un-checking) all the start up items, one kept being executed (the opening a of a .dmg file).
It's tough to test if the fixes cure the problem because I have to wait 3 - 4 hours before it will fail. Usually I just wait overnight because our G-5 is in constant us with two of using it to get actual work accomplished.
This morning I thought it would never start but after 84 loops it broke out. Before it finally breaks out, the next to last loop stays up for 30 seconds giving you the false hope that it is over then it goes one more time and it's up and running. And another interesting thing is that if I can't wait for it to finish looping, I do a reboot and all is well and it starts up normally.
I have run Tech Tools Pro on all drives and they are all OK. Ran diagnostics on all components of the system hardware and all were OK. I even ran disk repair and permissions on all drives and all OK.
Any other suggestions, observations or sources I can go to would be very helpful. My Apple care ran out a year ago so I can't go there.
Thanks for responding,
Al

Answer 1

Thanks for the rapid response!  This morning it took 89 loops to wake up.  The number is growing.
*+Also look in these if they exist, some are invisible...+*
/private/var/run/StartupItems
/Library/StartupItems
/System/Library/StartupItems
I did the above from your previous post and found nothing.  BTW how do you look for an invisible file?
Back under system 9 when the computer was doing things like this, we just rebuilt the desk top and it went away.  Now I'm not as up to speed on os x so do we need to rebuild the desktop from time to time and if so how does one go about doing this?
This morning, all of the startup items that I hid in systems preference/accounts appeared to work correctly as the .dmg did not open and did not appear on the desk top.
Another anomaly happening is from time to time I lose an icon (shows icon as a ?) in the tool bar but the application still works and restores the icon when you click on it.
I think I might have accomplished the same thing as safe boot by bringing up Tech Tools Pro from their emergency drive. After I did that I ran disk utility repair disk and repair permissions on all of my hard drives and it didn't find anything. All hard drives have been optimized last week.
My frustration is that it takes 3 - 4 hours for it to do the looping. Tonight, I will do the safe boot and see what happens in the morning. When operating under safe boot will I see my regular desk top with folders and files?
Now moving on. Is it possible and if so, how would I back out the recent security update and the QT update to see if that corrects the looping. Would going to os 10.5.6 fix this problem? I would like to stay with my current operating system. I realize that Apple has its' resources working on upgrading the 10.5 system and maybe things will get worse for us that are on os 10.4.x and wish to stay there.
I appreciate your support and that of others on this forum for without you, there would be no place to turn as Apple seems to be unreachable unless you have Apple Care.
Have a great day on this Super Bowl Sunday!
Al