Odd Electrical Issue with power windows

So last night I swapped out my alternator. After I got in the car, I realized that the master power window switch isn't working correctly. The "second stage" of the switch that's supposed to have them roll up/down automatically is simply doing the same thing as the first stage of the switch.
Has anyone experienced this?
I dunno, something funky may have happened with various electrical signals, but the staged switch was definitely working before my alternator went out.

It has to relearn. With window up hold the button down until you are full down. Then hold up until all the way up. Should work fine after that.

Ah, thanks. This is my first new-ish car (coming from a 90s shitbox), so I'm really new to a lot of these systems. Thank you, I'll try that.