The problem is caused by the fact that refresh rate changer and external player are doing to different things here. The external player resets the refresh rate set by MP because it says it is wrong for the content it is trying to play. Probably the Movie itself has a different RR than what is detected by mediainfo for the BluRay in general.

h4. Additional Information
http://forum.team-mediaportal.com/threads/call-for-tester-for-1-4-0-features-and-fixes.114566/page-72#post-984747