Step 1, if you're running Windows, check to see if its not any scheduled programs running(you're fucked if you are running windows
If running GNU/Linux, try to see what cron jobs are running, and monitor all your processes, have a cronjob that sees whats running and pipes it to a file
Step 2, try disconnecting your pc from the internet to be sure its not just something running an updater
Step 3, reformat your PC to be absolutely sure its software only
Step 4, if it turns out to still be happening, make sure oyu arent repeating your same software steps as you had, leave a base gentoo install running with xfce to be absolutely sure
Step 5 is really to get rid of the PC if you believe it is hardware