I have this same problem, but my "automatically switch" checkbox is not checked. What I do have is that I had Colemak as my only input source for a while, and when I added the English standard input source, the Alfred pop up box would swap input sources uses on every other use. I opened Alfred, found the Force Input setting to be blank, I chose Colemak and found that it forced the popup into the opposite (EN) input source, and vice versa when I set the force to EN. It certainly feels like some code is struggling to honor the sorting of the OS input settings.
