For some time now I've been noticing that the window issue with WinMX under wine is obviously ..... annoying. Well when I had did some modifications to GNOME and switched the Window Manager to Fluxbox, or Openbox I noticed that it went away. I'm assuming the WM switch handles "WinMX better"
Here is how to switch your WM in GNOME (since it's the most commonly used) to Fluxbox. With a little modification you can do it with any other WM.
# this is very simple
# note, you must have both gnome and fluxbox installed.
cp /usr/share/gnome/default.session ~/.gnome2/session
( for starters )
With your favourite editor
Depending on how it is setup for you..
Find this: 1,RestartCommand=gnome-wm --sm-client-id default1
It might be: 0,RestartCommand=gnome-wm --sm-client-id default0
( like mine was )
Change it to: RestartCommand=gnome-wm --default-wm fluxbox --sm-client-id default1
Then look for:
RestartCommand=gnome-wm --sm-client-id default1
Change it to: RestartCommand=nautilus --no-default-window --no-desktop --sm-client-id default2
After this, boot the session into GNOME and you shouldn't have any issues anymore.
Please be careful attempting this.