It seems like my problem is indeed related to ACPI, as I have read a
hint here earlier. I have switched ACPI off with "acpi=off" in the
kernel options and so far I haven't had any problem with the mouse or
keyboard. So, it works as a temporary workaround solution. And it should
help with finding the reason for the bug.

-- 
touchpad lockup/drag and lost scroll
https://bugs.launchpad.net/bugs/34501
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