@Stinto the restart probably did more to fix it than the ;fc-cache which only restarts the framework. Did you restart after it automatically installed you to 5.3.1? Or was your way to fix it - ;fc-cache - not working - install JB and JBPatch - works? It is entirely possible that the PW on 5.3.1 now only checks on a correct reboot if USE_ALT_FONTS is there or not - and a simple framework restart is not enough? I will go test that out and see what happens.
Edit: Mph that is not it either. Did not try with ;fc-chache, but from restart framework option from JBPatch, and it recognizes a deleting USE_ALT_FONTS and putting it back after the restart of the framework. So restarting only the framework should be enough. Remains a mystery