So, I did the throttle body bypass mod today, and when I took my car for a spin to test it (the TB is cooler then the previously connected insoluated hoses), I found out my window control is kinda funky. Oh, I had to disconnect the battery to get at the S hose, and that's probably what did it.
First thing I noticed is the key fob won't roll down the front two windows anymore. I used to be able to hit unlock twice, holding it on the second time, and the car would roll down the front two windows. That doesn't work no more.
The interior controls have trouble also, but this link should fix that.
https://www.mazdaforum.com/m_7649/tm.htm

Will that also fix the key fob?

 

You have to reset the windows. Just turn your key on (dont start). Roll down the driver window and roll it back up, but hold the button until you hear a click, should take a couple of seconds. Then move to the passenger window (not from drivers side door, passenger side door) and repeat. Repeat for all windows. Turn the key off, and then on again, and it should all be fine.

And yes, it will fix the key fob