@N9DRB
Not entirely sure what you mean with "dial in". Speculation: Twiddle the knobs of your manual tuner while watching your VNA to achieve minimal SWR with your chosen antenna, before replacing the VNA with the actual TRX. Is that what you try to do?
If yes, what could go wrong?
Strong signals coming in from the antenna might confuse your VNA.
@N9DRB
That's weird.
What did you have connected to the other end of the tuner? You could try connecting a heavy duty resistor of 200 Ω or 10 Ω or a normal 50 Ω dummy load. Then use the regular TX + SWR meter at low power to bring the SWR down. Now replace the TX with the VNA and see what SWR it displays, at the same frequency.