when defendants are sued for not paying contractual dues and they file for dismissal, does that constitute affirmative defense?

I think you're mixing apples and oranges.  An affirmative defense is a defense on which the defendant has the burden of proof.  Thus, in your example, if the defendant raised the defense that there was no contract, it would not be an affirmative defense, because it is the plaintiff's burden to prove a contract.  If the defendant raised the defense that the contract was unenforceable because it was procured by duress, however, that would be an affirmative defense, because it is the defendant who would have the burden of proving that the contract had been procured by duress.  A motion to dismiss on the pleadings (I assume you are referring to a pleadings motion; motions to dismiss can come at any time, and a motion to dismiss on summary judgment is very different than a motion to dismiss on the pleadings) can be based on either ordinary defenses or affirmative defenses, although they are normally based on ordinary defenses.  The defendant has the burden of proof on affirmative defenses, and usually cannot meet that burden on a motion based only on the pleadings.