I think the problem that you are having is that you assign a shortcut to a command in the menu by typing the command name in exactly as it appears in System Preferences. But in this case, suppose you have an account called "GMail" -- if you program a custom shortcut for "GMail," there is a GMail under Get New Mail and also another one under Erase Deleted Messages. So it isn't clear which one the shortcut gets assigned to, and it fails. I think that's the problem, but I don't know how to solve it. 🙁