Hi again Matt,
I just tried reassigning the keys in v.2.5 and it works fine.
What you need to understand is that the commands listen for a modifier. The functions can be triggered by any key (you can choose this), but modifiers are coded in the command.
You are either mixing things up in your message or have made a mistake while assigning those keys to the wrong command.
Center Markers (CM) in v.2.5 are created by 18 Create Magnet Target.jsfl as an alternative action.
So you need to assign two shortcuts to this command.
Shift+... will result in MT
Alt+... in CM
If 2 is your chosen key, then [ Shift+2 ] assigned to 18 Create Magnet Target will give you MT
[ Alt+2 ] assigned to 18 Create Magnet Target will give you CM
It can be Shif+5 and Alt+1 - it does not matter - the first will give you MT and the second CM, but you need to assign the keys to 18 Create Magnet Target
19 Smart Magnet Joint is a separate command, which deals with magnet functionality but does not create meta objects.
You can assign 2 to it and you will get the whole [ ` ] functionality of our set ported to [ 2 ]
Hope this helps!
Edit: 18 Aug 2015
Here is a link to a new article which may clarify the issue even further