If you look at the CNCZone site and do a search on ITX, you will see it is just as much a minefield as the situation with laptops. Some have no problems, some just don't work. MAybe it's being unfair to say it is as bad a the laptop situation but it is not all plain sailing if you go that route. The thing to do is to ask for recommended boards, ones in actual daily use and go for that.

If you were local to me, i'd bring my smoothstepper over for you to try, it would confirm once and for all where the problem lies and a fix for it.