While debugging a user script I came across this bug, which may be responsible for some of the issues occurring in the last time.
Tested MediaWiki version is 1.18wmf1, browser is Firefox 10.0.1. The script doesn't call document.write anywhere directly, so all calls to document.write are done by mw.loader.load.
I found several warnings in the web console, saying
A call to document.write from an asynchronously loaded extern script was ignored.
(translated from German, original: Ein Aufruf von document.write() durch ein asynchron geladenes externes Skript wurde ignoriert.)
So mw.loader.load should pay attention not to load anything by document.write unless this definitely can be done without problems. In this case several scripts were just missing.