It can be a heater control valve problem. The dual climate control heater control valve did have some problems in the 2000 model. Most times when this fails, though, the temperature shows a difference from the left side to the right side.
Whether it is temperature blend door issues, a heater control valve issue, or a control head issue - the best thing to do is get a diagnostic tool that can interface with the system and check out the components. Nothing in this system is cheap, so get it right the first time.