Alignment in MakerWare 2.4.0.14

Makerware doesn't seem to know where the left nozzle is. I've done the nozzle alignment built into the printer where it prints a bunch of lines and you tell it which align better.

Any dual extruder part like the pendant

Attachment 10779

Come out misaligned

Attachment 10780

I have "MakerBot The Replicator Dual" selected for the printer.

My antique printer:

Attachment 10781

Are there settings I don't know about, like in a file somewhere?

that's not just misaligned.
Have you definitely got dual extrusion ticked in the control panel ?

Well it's printed both wipe walls. So yep.

Weird, they are no nozzle offset settings that I know of.
That is odd.

I found a whole file of settings, but nothing about the relative positions of the two extruders.

Wondering if I should put sailfish on this.