I had a similar (the same?) problem with SS 3.0.5. I was loading jQuery 1.7.2 from Google's CDN in the Controller of one of my pages. (1.7.2 is the same version as ships with SS 3.0.5) This works fine on the frontend, but in the admin it ends up loading jQuery twice because the admin interface already loads the local version from thirdparty/jQuery/jQuery.js. The results were a bit unpredictable; sometimes it would work, other times not.
Having spent more time than I'd like to admit tracing round the javascript in the CMS, I think this was caused by the on demand loading of additional javascript when new pages are created. If I tried to create a page and the system determined that it needed an additional javascript file it would go get it but then fail to parse it (javascript parse error). In my case it was repeatedly loading ToggleCompositeField.js, I think the parse error was caused by having the second copy of jQuery which would have been pulled in in a previous request, hence the unpredictability; the order in which I was doing things in the CMS determined whether the issues appeared or not. Note that the error isn't in ToggleCompositeField.js, it's caused by having 2 copies of jQuery because ToggleCompositeField.js contains jQuery functions.
If you want to see whether this is the case for you add a complete handler to the getScriptQueue function in jquery.ondemand.js (framework/javascript/jquery-ondemand) like this:
complete: function(jqXHR, textStatus) {
console.log('getScriptQueue' + textStatus);
},
and watch the console in Firebug or Chrome developer tools. If you get parse errors, you know you got problems.
An oldish post I know, but this is the nearest I got on Google to solving my problem; hope that helps someone who arrives via the same route.