I've fixed this problem on my own before anyone replied. I am posting my solution in case anyone else is having this problem; please see the reply for what fixed it for me.

I've been using FGEMOD for a few days, and now for some reason my maps aren't compiling. I click the button to compile and preview the map, but it just puts me in this old map I compiled earlier. I was experimenting with replacing commands with aliases before, like puzzlemaker_save_dev, so at first I thought this could be the issue (like the alias got saved in the config file or something) but I checked the config file and it doesn't have the alias in it. Also, if I run the command it gives me an error saying unable to save file, which it's always done. How do I fix this?

SOLUTION:
I have the Sixense Motion Pack installed. Somehow preview.bsp got placed in portal2_sixense\maps, and the editor was saving to portal2\maps. When it tried to load the map, that one took priority. So all I had to do was delete SteamApps\common\portal 2\portal2_sixense\maps\puzzlemaker\preview.bsp and it worked.