Hm. It must be because I had manually placed the files in program files first, then dragged the .c2addon assuming it would replace the ones in program files, which it didn't. It also looks like C2 prioritizes the ones in program files over the ones in appdata. So it looks like the problem is in mixing the install methods. I do still think that a notification along the lines of "you have the same plugin installed in both program files and appdata, the one in program files will be used" would be a good addition.
In any case, I now know how to ensure that I'm running the latest version of my plugin, so thanks for the help.