first i'd check all your connections, generally a lock/unlock issue would be caused by a faulty constant to the brain, so depending on how your connections are made, i would look into this (generally happens a lot with t-taps).
Also, when starting with the key your ac/heat controls dont work? or is that when you remote start it? if its only when you remote start it that more than likely says one of your ignition wires coming off the brain could have a bad connection
or, the brain in general is bad.