I have updated the tags on the post for better visibility , can you let us know the model number of the micro gc?
I have actually the micro GC from Varian, CP-4900
It sounds like the TCD might be going bad on your channel 2. You can try calibrating the TCD within service tools to see if the red values go away. Also, make sure that the carrier gas that you have configured is the same as what is physically connected to each channel. Sometimes people get confused with the gas configuration on the micro, where carrier 1 might be going to channel 2 and vice versa.
If that doesn't work, my next thought would be sending it in to Agilent for service for replacement of Channel 2 module.