I think if you compare your version of /Controls/ScriptLoader.cs SetupClueTip method to the latest svn you can find the difference. My recollection is that I had to remove the document.Ready part from that script since it was registered as a startupscript anyway.
But really so much good stuff since that version. If you upgrade you get a lot of good new things. See the release notes for 126.96.36.199, 188.8.131.52 and 184.108.40.206.