Check your HD access light. If it's "on" your problem may be similar to mine: When my (old, failing) secondary HD controller "flubs" an access, and the kernel is waiting for the interrupt -- which never comes -- everything else is halted. (Sometimes the wait "times out" after five minuets, but then the "request" is reposted, and I'm back to "wait for interrupt.")
This is sometimes recorded in the log files in /var/log, but often not.
If the above is not your problem, try running a terminal window executing top (where you can see it) and see if it shows some process using all your resources when your "freeze" happens. (Of course the "freeze" will most likely happen when "top" is "paused," but you might get lucky.)
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