Fallout 3 Mother ship Zeta: Why wont i get abducted?

My guess is that it's a bug in the game that's causing the game to think that your Fallout character is not standing in that area. This is likely to happen because Fallout 3 is a big game and has a problem with glitches and bugs. If I was you'd I'd try and re-stall it. Backup your save data and re-stall the game.