Just a made a dumb mistake that might help someone else. I use a pedal board to select my presets in AT5 standalone. My preset folders were getting pretty messy so I went to the Finder and reorganized them. Great. The next day I came in and my pedal board wasn't switching amps. It had only been a day but I'd already forgotten that I moved the presets the previous day. They all still show correctly in the Control tab (would have been nice if they didn't). What I eventually noticed was, in the upper left, if I was on a preset manually, and then hit the pedal board, that area would flash and become blank.
The fix was simple, just go into the Control→Program Change area and reselect any Preset that was moved. Just moving the presets back to the original location and restarting Reaper didn't work for some reason. I had to re-select them.