I had a remote starter installed by Ziebart and the window doesn't go up automatically (it does go down automatically). By "hold full down/up" do you mean hold the window button all the way up for 3 seconds, then down?
Actually this happened to me everytime I worked on the stereo. However if you just keep using it it does go away.
Maybe it just took a while to relearn them by accident.
I'm not really sure why it happens, keep with them for a couple weeks and let us know.