Does OP have an entry on your taskbar?
My OP does the same thing - Sort of...
Starts loading, cuts to a resized desktop, at which point I have to click on desktop (switching it to Orig Desktop), then click on the Starfleet Command button in my taskbar. Doing that will start the game, but most of the main menu is off the upper-left hand corner of my screen... Luckily most of the "multiplayer" button is around so I can get on D2...
Note: system is a Win2K box, 1gHz proc., 128 RAM, GeForce2 based Video card - 64MB PCI