When you swapped boxes, you did boot with the fam20 diag key and in the clear menu, do an ultimate master reset to clear the NVRAM and Safe Storage?
If you don't, and that fam20 box was in your machine before. It will remember some settings so it may still boot. But if you didn't clear NVRAM and Safe Storage correctly after you put the fam20 box in there. Things won't work right, sometimes it will boot but give strange error messages until you do the clear and repeat machine setup again.
I've never seen Legacy Bonusing not show up in the setup menus under Protocols on fam20. It's in the same place that it is for fam14 in the settings.