Martin-
I'm having trouble reproducing your problem, but I'm just doing the basics:
1. Create a new web (on
http://localhost and VB)
2. Add a masterpage to the root (Masterpage.master, code in separate file)
3. Add a masterpage to the root (Popup.master, code in separate file)
4. Build / Publish Web Site, accept defaults and click OK.
I think it would be helpful if you could provide any info on additional steps you performed, and the contents of your masterpages.