I use Clock Override to customize the date and time format displayed in the top bar in GNOME Shell. Recently, after a couple of bad logins (Gnome crashing), it suddenly only reacted to the %S modifier and no other GLib GDateTime codes anymore. The date and time was either the default format, or the default format with seconds (when %S was part of the format string).
I tried reinstalling the extension, clearing its dconf settings and all that jazz, to no avail. In the end I tried to reproduce the issue using another user account, and, having failed that (i.e. the extension worked perfectly), once again went through bisecting a dconf dump from the non-working account:
dconf reset -f / && dconf load / <nonworkingThis finally revealed that Gnome Shell had set /org/gnome/shell/disable-user-extensions to true, which “makes sense”.
I might have found out the cause much quicker, had the extension not been in this bizarre “1 % working, 99 % not” half-state but completely nonfunctional. Even quicker still, had Gnome somehow indicated that it was now running in this crippled safe mode.