Every time Rig Manager downloads or installs an update it forces the progress dialog to the foreground. It stays there for the duration of the update no matter what application is in the foreground. This dialog should be attached to the Rig Manager process and only show up when it is in focus.
If the forum isn't the place to report this please point me in the right direction.
EDIT: I also noticed that when Rig Manager is processing, the GUI freezes up and certain dialogs stay stuck in the foreground as well (the "search in" dialog for instance).