I managed to run DF2JK on my Windows 7 64 bit computer thanks to the new .dll and the instructions from this page. Actual gameplay is fullscreen, menus and FMVs are windowed.
The only problem is that when I tell the shortcut from the JK.exe to run maximised (not really fullscreen, but effectively filling the screen), it only does it at the start of the game. As soon as I play and switch to the menu or get an FVM cut scene, I get the small 640x480 window again. And the FVMs aren't quite as epic when display on one tenth of my screen and with all my desktop item around (and not even in the centre).
Is there any way to force the game to leave the window maximised?