I honestly don't find it all that unusual for a horse to not like cross ties. I mean they have to stand perfectly in the center of the 2 cross ties, because if they don't there is more pressure on one side than the other. That's just my opinion though,
I do cross tie Vega, but that's usually only when she has hay/grain in her stall and I don't want her eating it until all her tack is off.
We don't cross tie Gem because he panics when he's in them, and since he's fine with us doing whatever in his stall, then we do that.