With the same column and liner the only possible cause of a different gas flow is a different pressure in the inlet. But NB that the inlet pressure might very well not be the same as the pressure measured by the EPC, since the EPC module sits at the other end of a long piece of narrow pipe. To verify the pressure difference you need to measure the actual pressures in the inlets - connect a needle to an ordinary pressure gauge and stick it through the septum. Supelco or somebody actually sells a pressure guage with a needle for this very purpose.

Just another thought, I have had problems trying to get very high split flows with glass-wool packed inlets due to the resistnace of the glass wool packing. Do you still see the retention discrepancies with open liners ?

Peter