Agreed.. with this being the case, the only thing (aside from a bug), that I can think of, is that these windows are using a format similar to that of creating a dialog using $dialog rather than /dialog. This is based (somewhat) on the following quote from the help file
Dialogs created with $dialog() are modal, ie. they halt the script until the dialog is closed, they return a value, and they don't allow access to other windows while the dialog is open.
