This happens when you remove some elements in Messenger's contact list. And it's not a bug of Messenger Plus!, it's a Messenger bug. It's well known in by old-school skinners and does also occur when you remove the code for the search-bar in the bottom of the contact list.
Never remove elements, just hide them using "LayoutPos=none" or similar methods. This will hopefully solve the problem.
You can read more about hiding elements here.
However it has been reported that there are other causes to this issue, but this is the usual cause.
/ 
