I ran my Oppo 93 at 1080p output for a while (to see if this reduced handshaking between trailers, menus and the film). This meant that I was sending 1080/50p or 1080/60p from DVD or certain BluRays through my Mini3D. I didn't suffer any issues with drop outs when doing this, so I don't agree that the Mini3D can't accept 1080/60p as an input, so IMHO the issue is something else (maybe a setting/cable issue, but not just the Mini3D input).
EDIT: Just to add that until recently I also had my PC connected to my Mini3D and the PC's output resolution was set to 1080/60p.
"Don't believe everything you read on the internet". William Shakespeare 1615