Is there any eway to disable scripts in one messenger but keep it running on the other messenger?

Thanks.

yes you bring up both of the preferences then choose from there (i have done it lots)

No, that is not correct...

The scripts are global, i.e. when you disable it in on one account, the other ones gets disabled too...

The only way is to let the script check if the current user is the user for which it should run

So you have to add in the script something like:
function Name() {
   if (Messenger.MyEmail == "email@server.com") {
      //Normal function...
   }
}
in every function...
Also make sure when the function runs, it is logged in, or else Messenger.MyEmail will fail, to check if someone is logged in use if (Messenger.MyStatus > 0) { etc... }

my way has worked many times before i have opened both plus preferences windows and gone to scripts and on the one you want to disable you just disable it and press apply but then do not hit apply/ok on the other one or it will be turned off too this is because plus does not constantly recall the registry settings.

i know this is a lot of work but it is much easier than adding more code into your script.

It will work sure...

But you'd have to do it everytime you startup WLM
Not very practical

So depending on your purpose, I would still go with my solution, or if it is one time only, go with Jay_Jay's