According to the ArcGIS Explorer (build 1500) help file when you capture a slide, you capture "Any popup windows that are opened and their size and position". When I try to capture a slide with a popup in it, it doesn't capture the popup.
Has anyone else had this problem? Am I doing something wrong?
You are probably trying to capture popup windows from service layer? If so, it won't work. There is a bug in AGX, and, hopefully, it will be resolved in the next release. Everything else should work just fine.