I believe the critter that starts at 4 HD already has the ability bonus factored in to its stats.
One thing I noticed about hero lab is that it cannot assign additional racial HD to a critter, only class level HD. (It is a character generator, and not a monster generator.) I believe this was addressed in another post on these boards, so I'm not complaining, just pointing it out.
So a 3HD critter that gains a class level should get an ability boost, just as if a 3rd level character gains a new class level.
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