The reason for this is because when you sign in to Messenger, the score variable is defined as 0, but it isn't actually set from the registry each time, so it will just continue from the beginning each time.
Change the sign-in function to this:
Javascript code:
function OnEvent_SigninReady(Email){
// Set score registry path
ScorePath = MsgPlus.ScriptRegPath + '\\Score';
// Set score variable Score = ReadScore(); // Start timer
MsgPlus.AddTimer('rato', 10000);
}