I had a bit of an issue one night with the polar alignment tool, and I found it was because the telescope information I entered was not saving or being applied correctly until I filled in a name for the configuration.
This information is entered on the Mount tab of EKOS. Enter the correct telescope focal lengths, Fill in the configuration name, and hit the Save Telescope Info button.
That will fill in the relevant details within the INDI driver itself. You should then save the INDI mount driver configuration from the INDI control window.
So try that. Save telescope configuration with a name and then run the Polar Align Assistant.

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