HELP: Irresponsive dock + menu + folder opening

Lately, I experience a weird behavior. Never had anything like it before. After a few minutes that my computer works just fine (15 minutes or so), the dock + application's menu become irresponsive, and furthermore, I cannot open any folder. A restart is then obviously mandatory. Actions taken so far include:
Getting rid of all startup applications - Problem persists,
Repaired permissions -> Problem persists,
Repair Disk (from a CD) -> I get "No problem found. HardDisks seems to be ok",
Repair Disk permissions (from a CD) -> Problem persists,
Checking specific applications - No candidate so far (although a certain Mathematica 7.1 file was used quite extensively).

Panther:
Given that the update couldn't validate, and that you've got a few Operating System-level error messages, I don't think it's your user account causing the problems. It could be a hardware problem, but probably not.
I'd recommend you attempt to backup, then Archive & Install (http://support.apple.com/kb/HT1710)
The backup will protect you in case anything goes terribly wrong. The Archive & Install uses your OS X disc and installs a fresh copy of the system software, without disrupting your user data and preferences. It does not erase the disk or your data. You'll need to run all of the system software updates after the Archive & Install, and if you have Adobe Creative Suite apps, you may need to reinstall those as well.
Hopefully, by installing a fresh system, the errors will go away. If not, your next steps are:
1) full re-image from your original discs
2) investigate hardware problems.
Make sure you back up!

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