On the ResidualVM forums, giucam has finally figured out why that happens.
Apparently, the LUA file for Domino's second speech has the same check name as the LUA file for Domino's first speech. So if you talk to Domino in his office at the beginning of the game, you won't be able to talk to him the second time near the end of the game.
The dialog options for Manny's second meeting with Domino are rather lengthy, and most people never got to hear them. So now, finally, Domino will no longer be sitting silently at his office at the end of the world. Manny can finally get Domino to take those darn headphones off and talk to him. ;)
Update (1/13/12): It is now no longer necessary to patch the file yourself, as ResidualVM does it for you. Download ResidualVM here.