I can only offer the suggestio that you look at how you sample the mixture for taking a portion to the main lab and then look at the process of dropping the pressure and temperature into the sample line. The vapor pressure of ammonia is high enough that I would not expect it to condense in the sample line, but if the gas mixture is allowed to cool before or in the regulator, I would wonder about some condensation - and segregation before passing through the regulator. I do not have a temperture/vapor pressure curve for ammonia to have an idea if this is likely.
If the regulator can take the temperature, it may be worth warming the line to the regulator and the regulator to see if the measured ammonia level changes.
And, if you can draw a sample from the sample line to the GC, you can take that sample back to the main lab and check for agreement between instruments. If the instruments agree on what is in the sample line, there is a difference in the samples between sampling points.