First of all, I'd like to to point to this thread, I'm Mikkel.
The problem occurs when changing the search setting to "entire library". This setting stays in effect without any issues until you select a Magic Node, at which point the setting reverts to "current selection" until a standard node is selected again (at which point it changes back to "entire library"). I'm using the latest versions of both MM (version 3.0.1.1127) and Magic Nodes (version 1.5.0.2).
I'm not sure whether or not it's a bug or incompability, nor whether or not it's MediaMonkey or Magic Nodes "fault". But I thought I better report it anyhow. I've also posted in the relevant Magic Nodes thread.