I don't know too much about him so I did some googling.
First, I think he's naturally a shorter distance guy anyway. Mile/5K. It's not unreasonable to think that someone in the NCAA might just outkick him at 10K. He won the 5K as a junior(?) so it seems like he's on track to me.
Second, how many footlocker winners have gone on to win NCAA XC anyway? According to Wikipedia it's Cheserek, Ritz, Torres, Goucher, and Kennedy. 5 guys since 1979. That's it. 5 out of 34.
There have been 5 guys that won Footlocker twice, but only 2 out of 5 (Cheserek and Ritz) won NCAA XC.
By the way, someone mentioned Rupp, who never won Footlocker or NCAA XC.
Overall I think there's a substantial difference between high school and college and there's no reason to be disappointed.