How do I fix disabled diacritical/accent marks?
If you look at the answer to a very similar question (but NOT a duplicate) you will see that the terminal work they suggest as an answer specifically targets the preferences for the given app - in that answer's case Terminal:

Accent popup in Terminal.app?

As a result, I'd start by suggesting you target the specific plist for the app you most frequently want this function in, and if it succeeds there, consider making that a system-wide pref.