I've tested the last patch to version 2.5.5486. It works good so far - except of one problem:
it seems to be impossible for the first try to close Milkdrop by a right click with "close visualizer". I always had to set it to full-screen by a double click first! That looks like a bug to me.
My Setup is a dual monitor one with expanded desktop. MB runs on the second screen.
Furthermore i would make some general suggestions for a more convenient and intuitive way to handle the visualizer:
The Option "Show in a Tab" should be renamed to "Show Visualizer Tab".
If "Show Visualizer Tab" is disabled, Visualizer only can start in seperate Window(/Fullscreen)-Mode and the option "Start inside MusicBee Window" (explained in 2nd below) will not be available then.
The Vis.-Options "Show in a Tab" and "Show in the MusicBee Window" should be merged to "Start inside MusicBee Window" > if enabled: manually collapsing the right and left side panels still give the option to change the integrated size. As soon as the Visualizer become undocked from the MB-Window (e.g. by double click), MusicBee should can be contolled normaly without closing or moving the Visualizer, even if the vis-tab hasn't the focus.
If "Start inside MusicBee Window" is disabled: Visualizer starts directly in a separate window and will be shown in full-screen on the preselected monitor. It could could be moved around and size changed also by double-clicking.
Expand the visualizer context menu (right clicking) by the entries are already under "Visualizer Dock/Fullscreen Mode": "Show on Screen 1/ 2 ... same as MB".
(here is a older thread about some of these thing already: http://getmusicbee.com/forum/index.php?topic=13379.0
How You are thinking about?