So whenever a menu pops up to have my confirmation of something (for instance, "Do you want to fast travel here?", "Do you want to craft this item?", etc.) the sounds still work fine, I can move the mouse around, and I can Alt+Tab myself out of the game fine, but I can never select on of the options. I've tried pressing enter and clicking, but neither works. This happens when I'm running the game in the SKSE launcher; I don't know if it does this if I launch it regularly out of Steam. I've got quite a few mods enabled and this seems to be the only major bug that I've found. Thanks in advance!

Did this just start all of a sudden? Has it always happened?

Have you tried a game cache verify? Good first thing to try.