Just in case this gets indexed by Google: I had a similar problem: JScript refused to function on the Checkout page, although it did function on other pages. I thought I caused the problem by being a bit too experimental with settings for flat fees, in combination with rules in workflow-ng.
The Misc directory had a jquery.js which after opening, turned out to be version 1.1.2. There was also a file jquery.bk01.js which turned out to be version 1.6. When I made the latter the active version, the problem disappeared. I liked that.
P.s.: Along the way I installed Firebug, as suggested above, but within the 10 minutes that I experimented with it, I wasn't yet able to identify the version of the jquery.js file being used.