Polarity is relative compared to the incoming signal.
Now that you know both switches are set the same, if you always use the same cables I would check that one of those doesn't have a polarity flip.
Initially if you are setting up by ear I wouldn't worry about a difference of six inches in placement. If you get a signal generator that can do a frequency sweep that would make it easier to hear if something is missing.
I would suggest setting up outside with your crossover in the same configuration/spacing you are going to use and running the sweep to make sure you are producing all frequencies fairly consistently. Then double check by playing your music.
If you have checked outside away from surfaces, when you move indoors and there is a problem and nothing else has changed in the setup then you know it is caused by the room.
Now that you know both switches are set the same, if you always use the same cables I would check that one of those doesn't have a polarity flip.
Initially if you are setting up by ear I wouldn't worry about a difference of six inches in placement. If you get a signal generator that can do a frequency sweep that would make it easier to hear if something is missing.
I would suggest setting up outside with your crossover in the same configuration/spacing you are going to use and running the sweep to make sure you are producing all frequencies fairly consistently. Then double check by playing your music.
If you have checked outside away from surfaces, when you move indoors and there is a problem and nothing else has changed in the setup then you know it is caused by the room.