I really don't know how else to say this in a sentence, but here's the gist. When I make a selection of any kind, while there is any colour in my secondary colour slot, then move that selected section elsewhere, the color in the spot where the selection was lifted from is changed from the standard 255/255/255 white transparent to a transparent version of whatever colour is in the secondary colour slot. So like, transparent green, or purple, or whatever.
This has the unfortunate effect of causing the magic wand to decide the colours are different (with 0% tolerance), and leaves dozens of artifacts behind whenever I've been working on creating frames for my pixel animation.
This has been driving me absolutely insane for the past few months.