What operating system do you have?
If it's Windows Vista or 7, is PT3 set to Run As Administrator? If not, the changes may not be saved to file properly (although if the changes aren't there when you re-open the window without restarting PT3 then that shouldn't matter).
ATTENTION: Windows VISTA and 7 users, you must read this...When you add stats do you see them appear in the list on the right hand side?
Can you post some screenshots of the before and after when you add stats so that we can see what you're doing?