I too am having this issue.  I wish to have a Slide Master for all Company
PPTs, and (after wasting half a day) have just found this thread which
exactly simmarizes my problem.  I do however get two guides left after saving
the POT file, but they are centerline vertical and horizontal, not the guides
I created for Graphic Placement..

The process described in the link is a marginal workaround.  I have had a
difficult time dealing with this, and wish this to be usable by those less
skilled than myself.  

I consider this a BUG

Steven