Hmm. Very strange. I'm not having any problems at all playing any of my mk4 (720P & 1080P Bluray) files on same equipment as MissBoxee:

-iPad ("new" iPad, 3rd gen) running iOS6
-Running Boxee Media Manager (on 2011 MacBook PRO)
-Storage is Synology NAS

Plays on iPad Boxee
And AirPlay streaming from iPad/to Boxee Box works excellent as well.

I do not have any loading delay (or blue circular spinning indicator) as you mentioned. Hope this helps.