Update: I thought I might add an update in case this may help future readers. I ended up realizing that my bench testing, as hard as I tried to make this as same as the final installation on the belly of my airplane, it was not close enough.
I originally had a DIY antenna that was using a 14ga copper radiating element. On the bench it tested 1.15:1. On the plane it measured about 1.4:1. The other aspect worth mentioning was that the antenna was close to the edge of the belly of the airplane. Like about 2 inches. Far from ideal.
I took a multi step approach to try to get better performance from my ADSB system. I originally had about 6ft of RG316 between the transmitter and the antenna. It measured about 1.2 DB loss. I replaced this with LMR240. That dropped it down to 0.25 DB. I tested this by seeing how well my positions were being logged by a receiver station about 45 miles away. It was a definite improvement. I was being "seen" at 2300ft.
Next step was to install a new antenna that was more towards the center of the airplane. Plus I used a SO239 with a 2mm copper wire for my radiating element and ensured it was about 1.2:1 SWR. This turned out to be another step in the right direction. I was now being captured by that same receiver but now as low as 1800ft.
My system now performs every bit as good as other systems costing thousands of dollars more.....
Having the Nano VNA allowed to to measure the system so much more accurately that the old needle analog tool. Plus I was able finally to accurately, easily measure DB loss.
While I never satisfied my curiosity for the difference of SWR readings that I originally posted, I did end up with a noticable improvement of my system which really was the most important goal.
Thanks for the suggestions.
Charlie