Hey Patchou, ever since I got my laptop I was wanting to test this and today I had a few minutes to do so.
I opened the Plus! preferences window and closed the lid of my laptop. This caused my laptop to hibernate. So once the laptop was off I opened it back up turned it back on and the Plus! preferences will still there (obviously) so I stopped MSN Messenger 7 from signing back in and I had full control of the preferences window although I was not logged in. So I unchecked all the plugins then clicked Apply and it said the normal messages. I decided to go to the POP3 and check that; all the info was still there so I removed the password for it and clicked Apply. The password was gone but something weird happened. Instead of staying at the POP3 Checker screen it went back to the Plugin Screen but POP3 Checker stayed highlighted.
Needless to say I hit ok and logged back into MSN Messenger and surely enough all of the options I had just changed were in fact changed even though I wasn't signed in.
Windows Version: Windows XP, 5.01.2600
Messenger Client Version: 7.0.0425
Messenger Plus! Version: 3.40.0112
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Possibly a way to fix this is check to see if the MSN Messenger client is logged in before saving settings... oh well you will figure a way around it, your the expert programmer
Matty