The problem is that any addon that tracks all of your characters does it by storing data in an account-wide file, I believe:
[WoW dir]\WTF\Account\[Account]\SavedVariables\[Addon Name].lua

You can make all of your characters seem like they share the same WoW account by symbolically linking the [Account] directories to a common location, but changes from one copy of WoW will overwrite ones from another copy when you log off. I don't believe that there is any way in the WoW API to either load or save addon settings on demand so that you could avoid this issue.