Haven't been able to make a specific use case that replicates this, but best success in duplicating it was to add a few stops and step through code that will step back and forth through multiple files (i.e. your code and jQuery code.) At some point, one of the scripts will not clear from the script panel and anything else you view in the script view is overlaid with the "stuck" script. At the link (Firebug bug report) there are some screenshots showing the problem.
http://bit.ly/ogHey1