Some internet service providers do packet throttling. Basically artificially inflate the ping by a few seconds to throttle peer-to-peer connections. With a windowed mode I'd be able to do other things while waiting for the server and battle animations.
Fair point. If you launch the game now it will patch to a version which can switch between windowed and full screen mode. On the settings screen (use the settings button from the party select screen) you will now find a button labelled 'Toggle Windowed Mode'. Use that to switch. The game remembers your last used mode and will start that way next time.