Emma,
Your detector is a TCD?
You are using nitrogen for the carrier or helium?
If you are using helium carrier then you will not detect helium in the sample.
If the Porapak Q in the outer shell is in good condition then you should have a small separation of helium and methane. With nitrogen as the carrier your response for methane should be quite small. Helium should have excellent response. If your carrier is helium then methane will have a high response and helium will not be detected.
Helium and methane should separate by a large amount of the molecular sieve inner column.
Unfortuntately, at least to me, your sample matrix and the carrier you are using are not clearly defined. This effects any answer I or anyone else may try to offer you.
Please restate your method, conditions, detector, temperature, sample size injected, and the amount of analytes in your sample.
best wishes,
Rod