Does anyone know if there is a reason why simple javascript won't work when browsing from the same machine that is running web companion?

I'm running 5.5 developer, writing and testing a CDML web app from the same machine (mac) I've got a button that calls a simple popup window javascript - it works flawlessly on PCs and other Macs, but when I try to browse the page from IE on the mac that is running web companion, the javascript freezes IE. All other javascript seems to work fine (outside of the pages that are being served by web companion.)