Figured it out. My INI Path was screwed up. made sure it was relocated to my actually game file location. (Example: Users>*username*>Documents>My Games>Fallout 4) Just incase anyone else runs into this aswell.
So I just downloaded BethINI for FALLOUT 4, tried tweaking a couple of settings and this popped up as I tried saving and exiting. Tried it a couple more times and still the same message will pop up. ill even simply open BethINI and close it without altering anything and it will still show this message. please help