I also thought that might be a hardware problem (in fact I still consider it), 
so I did a memory test.
One and a half pass and no errors found.

I have 3 HDD on my machine.
First I installed twice 9.04 beta then RC on the ATA one.
Always after second reboot system was starting extremely slow, was runing 
auto-fsck saying that there was unclean  shut down (there was now unclean shut 
down in fact). Then I always had to do manual fsck anyway - There were always 
tons of errors. And it happened many times.

Then I decided to try 8.10 - exactly the same - self closing
applications, fsck after each reboot etc.

Then I decided to switch to the other HDD and installed 9.04 RC on my SATA.
Two reboots and it was fine.
Third reboot - self closing applications, again :(
Another reboot everything was fine... after an hour - freeze.
Two more reboots - all is fine so far


Attached kernel.log:
  Apr 22 21:18:06 Tester kernel: [  263.572111] apt-check[3521]: segfault
  Apr 22 21:20:18 Tester kernel: [   17.502242] PM: Resume from disk failed.
  Apr 22 21:21:21 Tester kernel: [  103.046654] ondemand governor failed, too 
long transition latency of HW, fallback to performance governor
### There was this latest freeze here  ###
  Apr 23 20:40:57 Tester kernel: Inspecting /boot/System.map-2.6.28-11-generic

And also kernel.log.0

** Attachment added: "kern.log"
   http://launchpadlibrarian.net/25900516/kern.log

-- 
lots of freezes and segfaults
https://bugs.launchpad.net/bugs/358741
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