This is not my problem, it is a friend's so information is limited.

She said that her all running scripts are being disabled when she restarts her computer or messenger (I am aware here is not clear but she is too lazy to say which one is restarted for scripts to disable themselves). She have to tick all scripts again from Plus! Preferences after each restart.

How can she solve it?

By

1) Shutting down messenger properly before shutting down

or

2) Shut the computer down correctly and not just hold the power button in until it switches off

They would be the first things I would make sure are done correctly. Otherwise try and find out what programs have been installed recently, maybe there is a conflict somehow.