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Im running system encryption on my laptop with truecrypt. Every time it comes back from sleep, and then randomly every hour or so, it will freeze up for 30-50 seconds. The mouse will still work, but clicking on anything will not. After the lag is over, all the clicks made register and the computer comes back to normal.

Removing truecrypt system encryption fixes the problem.

Is there anything that can be done to get it to work with trucrypt?

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What kind of disk are you using, i have one of the early Intel SSD disks and those freeze up when they get nearly full.

Moving on you should use some kind of system monitoring tool, to see what the system is doing during the freeze :

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