I think this is not the case, because my mouse is connected to the PS2 port and it is moving fine during lag, only system and apps do not respond (when i hover over a button or do the click or scrolling web page mouse moves, but not scrollbars - lag), also the music playback is lagged at that times.
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Well, if MX is installed on your internal hard drive and not running off of a USB stick/drive like your torrent and crypt are, then it can't be a USB buss issue.
USB 3 should be way fast enough to handle the bandwidth from a spinning disk.
Have you tried nicing the IO like Felix suggested? When you kill the HDD and the encrypted drive and remove them, does the problem go away or does it still act sluggish?
Son, someday all this will belong to your ex wife.
The Liquorix kernel touts itself at being more responsive, so I wonder if trying that (keep your present kernel as a backup!) would make any difference.