I'm not sure what changed, I don't remember changing anything in Preferences, but for some reason now when I ctrl+click an alpha channel's thumbnail, the selection is inverted from what it should be. Before, when I ctrl+clicked, it would select the white pixels, allowing me to go back to my layer and add a layer mask so that only what was white in the alpha channel would show up. Now when I ctrl+click the alpha channel, the black pixels are selected and I have to either invert the selection, or add the layer mask then invert it. What's really weird is that if I then ctrl+click the layer mask channel in the channels tab, it correctly selects the white pixels, like it should with the layer mask. Also, if I click Selection > Load Selection and choose the alpha channel, it still selects the black pixels, unless I check the "Invert" option. I didn't used to have to do that.
Does anyone have any ideas as to what I might have changed to make this happen?