This is possibly a bug in Hero Lab but it's been pretty solid so far; so I'm trying to work out what it's doing. If it is a hero lab bug, then this question will probably need to be deleted.
I've created a Tiny creature race template with a racial dex mod of +4. The PC in question has a base dex of 10, with racial this gives 14 (+2) The creature also has a natural armour mod of +4 (It's a dragon)
But the base AC of the creature is listed as 17 (+1 dex +2 size +4 natural)
(This has also affected CM defence in the same way, incidentally)
The initiative modifier for the character is (correctly) calculated as +2.
The character has no armour on or any other effects I can think of.
So; the question (finally!):
What, apart from armour, can restrict the dexterity bonus to AC?