Is it only MP!L or it happens without MP!L. Do you have anything else related to WLM installed except MP!L? Try removing that might solve your problem. If that doesn't wopk heres a temporary script to solve your problem.
code:
function OnEvent_ChatWndReveiveMessage(ChatWnd, Origin, Message, MessageKind){
Interop.Call("User32", "FlashWindow", ChatWnd.Handle, true);
}