I'm using Windows XP and the Steam version of Aquaria.
After losing once against the final boss, I decided to pause, then skip, the opening dialogue. I approach him, press Start (I'm using a 360 gamepad) - and the game hangs. Pressing S does nothing, I can't hit Start again to resume the scene, and it doesn't respond to anything else I press. I can alt-tab out of the game and kill it from Task Manager (where it says the game is "Running"), and alt-tabbing back it takes me to a black screen. I've done this twice so far, so it's reproducible on my machine.