There is a registry option to stop this
http://www.msgpluslive.net/help/registry/
HKCU\Software\Patchou\Messenger Plus! Live\
your@email.com\Preferences
EnableScriptProtection
Boolean value.
Set to false (0) to disable automatic script disabling when Messenger ends prematurely.
Obviously if that Boolean is not there, right click "New -> DWORD(32bit) Value
or
Open Notepad, paste the following in
code:
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Patchou\Messenger Plus! Live\YOUR-EMAIL-HERE\Preferences]
"EnableScriptProtection"=dword:00000000
Save as a .reg, double click it, voila