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.
It is really best practice to select the scope information in the equipment profile itself, and try to avoid to use the Mount tab to set them. That was there before we introduced the scopes in the equipment profile, so it might get removed at any time.
I don't quite follow. "Equipment Profile" could mean a few locations in KStars where I can enter telescope information. But as far as I was aware, I only found information entered in the mount tab or directly within the INDI driver itself populated the scope choices available in the align module. Is this something very new, or do you mean Telescope Selection in the Profile Editor? I didn't notice the telescope selection in the profile editor doing anything.