Today I actually had a client's PC exhibit the same symptoms you mention Egghead.

I have not yet found a solution so I'll be keen to get to the bottom of this. The PC is running Windows 2K SP3, IE 5.5 SP2. No other PCs in the immediate area (same config) are having this problem. There are no pop-up blockers installed on the machine either.

Problem: Javascript popups fail to load. Example of the type of pop-up here. (Click the picture to see the pop-up.)