Irresponsive menu + dock + 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).

I see two possible explanations.
1) subtle memory errors
You could run a long diagnostic overnight, but the problem is in the spot where a crucial part of the System loads, so you may not find out anything.
I suggest you shift your memories. Take the rightmost DIMM out, move the remaining DIMMs to the right one slot, and put the old rightmost DIMM in the leftmost slot. Then try again and see if anything has changed.
2) damaged system files.
The "fix" for that is an archive and install, if you have the space on your Hard Drive for another copy of the basic system. It is always a good idea to have a backup before starting this process, if possible.

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