Hi @tcmesserschmidt,
The base position in the RINEX header is the last averaged epoch coordinate with an accuracy of a few meters. It is different from the one averaged in Emlid Flow. Thus, your RTK and PPK base positions may differ by several meters.
In the CSV file, you can see the base position used during your survey. And Rover used it as a reference.
I agree with @daygeckoart 's ideas on how to improve the accuracy.
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You can process the data in PPK using the corrected base position from OPUS.
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Or you can shift RTK data based on the calculated difference between the old and new base positions. You can read more about it here.