What CPU usage does  Qubes Manager show? I guess is shows low CPU usage.

Do you see any other symptoms of high CPU usage like heat or fan activity?

I guess the Xen just allocates some CPU time for some VMs, but the time is not 
used. As a result, xentop seems to overestimate actual CPU usage.

Regards,
Vít Šesták 'v6ak'

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