I've found a rather strange but effective, at least for me, workaround for the issue.
1: open a terminal and sudo sh
2: apt-get update && apt-get dist-upgrade
3: cd /boot
4: nano /boot/config.txt
5: insert whatever overclock settings you want.
6: save the file then run sync
7: cp config.txt config.txt.save
8: cp config.txt config.txt.save.1
9: sync; sync; exit; exit
10: After 9 is done move to another tty CTRL + ALT + F2
12: sync; sync; shutdown -hP now
13: unplug and replug
I know it's kind of a wonky workaround, but it seems to be working for me. I forget what it was I was doing exactly, but the terminal shouted at me that it was having issues with the config.txt.save file. After trying a few different things this craziness is what I found to work.
I have noticed if you set your values too high it will still corrupt your config.txt file. Don't ask me why I'm still taking baby steps in this whole admin thing.