I can't guess why Samsung does that and not to the last input. It's been reported all over so why you write there is nothing wrong with the TV it does appear to default to the wrong input.

Did you try disabling that port? Most Samsungs don't allow this.
http://forums.cnet.com/7723-13973_102-327199/removing-tv-from-source-list/

Call it in. Seems to be some thing everyone wants.
Bob