This app was mentioned in 3 comments, with an average of 1.33 upvotes
Problem solved. Should have been obvious, I suppose, but I did not see the setting in the app that was causing this that was changing the tones. The culprit was Audio Manager Pro a great app for setting up volume profiles. Turns out, those profiles can also change the tones from the default. So basically a d'oh and duh moment there.
Nope, I mean this: link
It was audiomanager pro: https://play.google.com/store/apps/details?id=com.smartandroidapps.audiowidgetpro&hl=en
But from what I've heard, any audio manager could likely cause the problem.