Yep, I tried the long reset as well.
After further, closer inspection tonight, the top edge of the passenger side window is a noticeable amount further out from the car compared to the drivers side window. It is probably 1/8 of an inch, but enough so it is not aligning perfectly with the rubber door / window seal.
I assumed the door panel being removed yesterday for the speaker install caused the window's electronics side of things to have an issue, but looking at the window, I am leaning towards it is actually an alignment issue with the glass and it was already like that before I installed the speaker.
Phoning the dealer tomorrow and will get them to look at it.
Thanks for the tips / help - I will update the thread when I have one.
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