What level is it?
This happened to me once - sometimes when the level is high enough the stats go pretty high and vitamins are deemed useless - the only way to raise the stats are to level up. I had never used a vitamin on the Pokemon once, and it wouldn't 'have any effect'.
I can't say it can't be anything else - Flygon is somewhere at like Level 50, so I think I'm right. x)
Sorry :(