Methane quantification issue - Agilent 7890a

Hello, I am using an Agilent 7890a to quantify hydrocarbon reactions. Samples are introduced to the GC from our flow reactor using a sample loop and 6-way valve. We flow methane at room temperature prior to reaction to quantify the starting amount of methane, and use the peak area during reaction to know the amount of methane that was consumed. However, recently the methane peak area during reaction ends up being higher than during the room temperature conditions. Does anyone have ideas as to what could cause this? We see plenty of products so we know methane must be consumed during the reaction.

This problem does not persist for other hydrocarbons, just methane. We thought originally that the methane overloads the column, but the issue has persisted even after switching to a small sample loop and increasing the split ratio, although the methane peak is a good shape with no tailing. 

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