The fix would probably be similar to
https://www.mediawiki.org/wiki/Special:Code/MediaWiki/64670

OutputPage::makeResourceLoaderLink should handle this properly, I'm looking into why it isn't.

https://github.com/wikimedia/mediawiki-core/blob/master/includes/OutputPage.php#L2726 isn't checking TYPE_COMBINED, which our global user module is using.

Change 149185 had a related patch set uploaded by Legoktm:
Check whether TYPE_COMBINED modules are allowed to be included in the page

https://gerrit.wikimedia.org/r/149185

Change 150442 had a related patch set uploaded by Legoktm:
Use OutputPage::addModuleStyles/Scripts to add modules

https://gerrit.wikimedia.org/r/150442

Change 150442 merged by jenkins-bot:
Use OutputPage::addModuleStyles/Scripts to add modules

https://gerrit.wikimedia.org/r/150442

My global CSS is loaded on Special Preferences (both on Meta and other wikis).

On
https://meta.wikimedia.org/wiki/Special:Preferences#mw-prefsection-rendering
I get this in the console (on Firefox):

mw.loader.getState('ext.globalCssJs.user') === "registered"
true

and
https://bits.wikimedia.org/meta.wikimedia.org/load.php?debug=false&lang=pt&modules=ext.globalCssJs.user&only=styles&skin=vector&user=Helder.wiki&version=20140826T153947Z&*
is still loaded.

I can't reproduce right now, but moving to the security component just in case.

Okay, I can confirm my global CSS is being loaded, but not JS. Investigating...

(In reply to Kunal Mehta (Legoktm) from comment #10)

Okay, I can confirm my global CSS is being loaded, but not JS.
Investigating...

See bug 70672.

This is fixed with the patch applied in bug 70672.