Perhaps, problem in using realtime kernel. I've back generic kernel and my 
shutdown works properly, also suspend to ram and disk works properly. I'll test 
it while and will write here about results.
Why I think on rt-kernel? In attachments in syslog can be found BUG: entries. 
With generic kernel I do not see it.

** Attachment added: "bug.log"
   http://launchpadlibrarian.net/19562290/bug.log

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KUbuntu 8.10 Intrepid freezes machine after some time of inactivity
https://bugs.launchpad.net/bugs/296306
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