The computed split rate on the GC assumes that you have given the correct column geometry and the column is installed in the inlet. And, it assumes that vacuum correction has been set to match the installation of the column. (I don't know the term Varian wojuld use for this correction. If the column outlet is atmospheric pressure, the vacuum compensation is off.) And the correct gas must be specified in the GC configuration.
If you have removed a bit of the column - that can affect the calculation. A few CM from the end of a column, you can usually ignore. But loss of a couple of meters needs to be reflected in the value in the instrument configuration.
Measurement of flow with a flow meter must be done correctly. There needs to be a good seal between the outlet of the GC you are measuring and the tube leading into the flow meter. If your trying to measure the flow coming out of a column by pinching a rubber tube around the end of the column - it will give you an accurate reading. There will be flow along the end of the column and out into the room no matter how hard you squeeze the tube. (I've tried it.) Typically the flow from a GC column is measured through the detector with an adapter that gives a tight seal into the detector outlet and with the tube to the flow meter.
And the system should be leak free.
Measurement of gas flow out to the split vent and septum purge also need good connections. Add empting to push the tubing from the flow meter over a threaded fitting does not work. And, I don't know the fittings on the Varian instrument.
And, as Peter notes - electronic flow meters are sensitive to the type of gas being measured. So be sure that it is set for the correct gas.
