Short and sweet: To eliminate screen flickering and the disabling of a multi monitor setup my suggestion is full screen windowed mode (ie: a window with no border and can't be moved).
Maybe an easier suggestion would be resolution options that take into account the screen lost by the window border and the task bar.
Phishbreath
you can go into full screen mode, you just change your resolution to match your screen.....
I believe this is possible and what u are talking about.. since my spiral knights is run with no boarder etc.....
options *escape*
first tab *general*
at the top of that called 'screen resolution' change it to fit your screen fully.
i believe that will work