Sometimes it is best to use a memory saver when battery needs to be disconnected. Any system that uses memory if that memory is lost because the battery was disconnected, there may be problems when everything is hooked back up.
Can you check for any applicable hvac codes? Your hvac may need to be reprogrammed, where applicable. I'm just going by the fact it started when battery voltage was lost by disconnecting.
Sorry for the late reply.
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Sunday, March 15th, 2015 AT 10:39 AM