I have the exact same problem but I found a way to circumvent it.
I realized out that you can stop Manny dead in his tracks by accessing his inventory. When I reach the end of the conveyor belt, I wait until the screen goes black and then start mashing the inventory keys. You can try pressing only two keys with one hand—such as 1 and 2—like a piano trill, or mash many of them at once with two hands—such as 1, 2, 3, I, and D (it helps if you have 3 items in the inventory, or the three won't do anything). Try to press them consecutively, rather than simultaneously. You'll need to be really fast to keep up with your computer. This method isn't surefire, but it's consistent.
I'll have you know, however, that my computer's slow by today's standards (750MHz CPU), so CPUs in GHz may be too fast for human fingers. Also, you get a 'free' trip to the ship if you go down after the cutscene that plays when you enter Domino's office for the first time. A scripted sequence will override any other action, and direct Manny towards Glottis.