Okay, something definitely isn’t right.
Before:
http://puu.sh/jJoBA/33d5c4a64c.png
After:
http://puu.sh/jJoGm/27bb8c16a4.png
As you can see, it also messes up the Google fonts part.
What’s the version number of the Theme you are using? 999 comes from that. I’ve made some improvements in version 1.2 which may improve things.
I need to change the code at some point so that the inline version number is parsed out from the existing ver= and inserted inline, instead of globally assigning the theme version number. My bad.
So your plugin uses the version of the theme for all scripts and styles? Does this make sense at all?
I ended up using this plugin here which is working perfectly:
https://dominikschilling.de/schnipsel/wordpress-cache-busting-versionierung-dateinamen/
Resolved through an update to v2.0 of the plugin. v2 uses Dominik’s code, ported forward with the GLP v2 license.