This is still build 231 not the current beta.   But I installed office 2010 today and thought I'd try out some of the ppt's in the beta folder.  (Background info) Clean install of 231 so I forgot to set the overlay to 800x600.   So it went full screen on me.  Normally I use 800x600 overlay to check scripts without a second monitor attached.  This may have been going on before just never saw it.  

MS setup: viewers are set to program and preview.  Overlay is set to full screen (by accident).  ppt 2010 is set as the editor and player.   Areo is disabled through MS settings.

Here are the steps to recreate the issue.   Start new script,  insert ppt 1,  then insert ppt 2,  then insert a black cue.   I used If we are the body and awesome God from the dropbox beta folder.  Fire cue #1 and then hit ctrl+shift+O to start the overlay.  and spacebar through the ppt.  The start ball/button will flash during most of the transitions.  I also had windows media player classic up in the background.  It had just finished a video so it is yellow.  I would see it also.   I didn't see anymore things in the taskbar just those 2.