I believe that the most recent workbook to be opened gets the shortcut key assigned (it overwrites any previously).
You could deal with this by using code to assign your macro to the keystroke in the Workbook_Activate event. That way each time the workbook is activated it would re-asset control.
I know you post at other forums, and it's been a week since you posted this. Have you got a solution yet and, if so, would you mind linking to it or posting it here? If not, we'd be glad to help.