I have a 2006 Mustang GT, I replaced the SJB and got DRLs (not concerned) as well as now my key fobs will not pair what so ever. Other than that I don’t have any differences or issues with the car, the batteries have been replaced, they worked before I removed the SJB and installed a new one.
I have programmed multiple fobs to this car over the years so im aware of how to do it.
it goes in to programming mode but won’t accept any fobs for some reason.
anybody have a solution before I take it to the stealership to figure it out?
I read another forum about having something plugged in to the aux and it interfering with the transmitter, that is not the case here either.

 

The replacement SJB having DRL and you're original not, might be an indication that something else is different too. It should just be plug-n-play as in swap the parts and no programming of anything needed.

You'd have to have schematics for both SJB's to see if it makes a difference or not.

Why did you replace your original SJB?

 

I replaced it due to the notorious passenger side water leak, which is now fixed.
My original SJB was starting to short. I replaced it nearly a year ago and it has been my daily, other than that there is not a single difference.