Shoutbox

It works fine here though...
Make sure you have set the correct options...

To only be notified for certain contacts:
Disable:
Tools > Options > General > "Display alerts when contacts come online"

Enable:
Plus > Preferences > Notifications > Popup Options > "Enable Messenger Plus! notifications windows"

Plus > Preferences > Notifications > Popup Defaults > "Enable Messenger Plus! notifications when contacts sign in"

Now, for every contact you can select the notifications you want to show up:
Right-click on a contact > Messenger Plus Extras > Notifications > ...

Contact goes offline: Show a notification if that contact goes offline
Contact's status changes to: <something> (note that selecting "any status" or "online" will popup a notification also when the contact comes online, even if you disable "contact signs-in")
contact signs-in: Show a notification if that contact comes online

Notify me next time: Only the next time the contact changes his status (according to what you've selected above), you 'll get a popup.
Notify me each time: Each time the contact changes his status (according to what you've selected above), you 'll get a popup.

To only be notified by MSN Messenger, and only when a contacts sign in:

Enable:
Tools > Options > General > "Display alerts when contacts come online"

Disable:
Plus > Preferences > Notifications > Popup Options > "Enable Messenger Plus! notifications windows"

Plus > Preferences > Notifications > Popup Defaults > "Contact goes offline"

Plus > Preferences > Notifications > Popup Defaults > "Contact changes his/her name"

Plus > Preferences > Notifications > Popup Defaults > "Enable Messenger Plus! notifications when contacts sign in"