Marciano when he fought Don Cockell Didn't seem to go well for him either edit: Sam McVea vs Sam Langford is another that comes to mind
He was fighting at a lower weight at that time, and pretty regularly fighting shorter people, like Gans and Elbows McFadden
Possibly Lavigne vs Walcott, but I haven't really checked. Actually Lavigne commented he thought being shorter helped him beat Walcott due to being able to go to the body more, so perhaps though he wasn't as short as Walcott, fighting someone closer to his height was a hinderance.
True, not as short as Walcott, but I think that was more because Walcott was unusual, he was fighting a good few Lightweights and Welterweights at that point. Langford was certainly used to using his longer reach and fighting at range.
Orlin Norris is another fighter that was shorter than Tyson that had some moments against him. Both Norris and Mathis Jr. were pretty skilled guys.
James Toney at 5'9 was usually the shorter man in the ring especially as he moved up in weight. 5'7 Montell Griffin gave him fits in there two fights. I still think Toney should have won both fights but would not argue with anyone that saw it differently. Both fights were close.