Would love to help, but it is big WTF for me. I know it isn't most bright advice, but 100% clean reflashing could help filtering out software issues. I'm worried, that You might be experiencing signs of hardware problems, and it is fastest way to check it.

If You decide to do so, please use it for a while without installing anything, and check if problem returns. Then, You may install/recover backups etc - after every step, check if You get this problem again.

/Estel