My guess is they're saying "Since I'm going to court anyways, might as well file a counter-suit to get the one month back for the inconvenience" or something along those lines. I don't think they feel like they can win the counter-suit, but might as well try since I'm taking them there anyways. Just my thoughts.
If i were you i would try to keep this out of court. They could win their countersuit depending on the Judge you get. He could try to "teach you a lesson" for handwriting in a poor lease clause. Judges also try not to award security deposits to be used as any kind of penalty fee. I would tell them I'll drop the suit if we go back to our agreement of 1 month and the security deposit. And remind them you have proof of their agreement to that settlement.