Hmmm... That's pretty weird. I don't know why it would do that. Anyone else have an idea?
Speakers create noise by pushing or pulling air to create vibrations. If one speaker pushes at the same time another one pulls, they cancel each other out. This is referred to as phase. If all speakers push exactly the same, they would all be at the same phase. If one pushes while another pulls (at exactly the same time), they are 180 degrees out of phase. If the speakers are 180 degrees out of phase with the subwoofer, switching from normal (0 deg) to reverse (180 deg) will reverse the direction of the subwoofer, removing the out of phase cancellation.
Generally speakers are out of phase when they are wired backwards (positive terminal to negative wire, negative terminal to positive wire), so in this specific case it is likely that the subwoofer is wired backwards, though it is possible that both door speakers are wired backwards instead. It is only affecting the bass because a subwoofer doesn't produce high-frequency sound, so it won't cancel out anything that the front door speakers do above its frequency limitation. There are other things that can cause phase issues, but this is the most common issue. I hope this helps!
Possibilities:
1) You do not pay attention while installing (even pro shops do it - I know because I've corrected their goofs for people)
2) Also Just because you buy a brand name, doesn't always mean what you think it does. The X-item is generally manufactured at some location to specs and if they mess up and mark positive/negatives backwards (more common in speakers where they use a red DOT (paint or sticker) to indicate +) and print wrong wiring diagram, then you wind up 180° out of phaze. I always use a multimeter to double check what the diagram says after I install it. I know blowing over $83 on 'checking' a system is a bit steep for most... but there are a lot of cheaper units out there with limited functions that will show if you are truly getting + & - correct.
Couple quick points -
Phase issues can be caused simply by the distance between the speakers - if the subs are in the trunk, the sound might take 1.5x as long to reach your ears as the sound from the door speakers, resulting in the sound being out of phase.
I don't have it bookmarked, but Carolinasp3 had an old post that said tweeters and woofer in component speakers were supposed to be out of phase for some reason, but the manufacturers did it internally so when you wired it in phase per the diagram, it was really out of phase, but that was intended.
I paid around $3 for my multimeter - well worth it.
2002 Ford Focus Sony CDX-GT410u Sony XT-100HD HD Tuner Stock speakers, no amp, no subs