I'm at a loss of what to suggest. Same cables, generator, scope, splitter, PC, USB port, software... Scope and splitter resting on a ground plane next to my VNA. The setup wasn't taken apart between tests. I wasn't playing with my spark gap transmitter, ignition systems or anything else I would expect would cause a disturbance.
The only thing that has really changed is or course, its a different day and the office temperature was lower. As you know, I had tried to look at the stability with temperature but at that time we did not have the new FPGA/firmware. I plan to repeat these tests once your software has evolved. Maybe that has something to do with it.
Let me know if you have any ideas.
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If the setup is not clear, see attached sketch.