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

alignmentB.jpg

Come out misaligned

alignment.jpg

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

My antique printer:

paleobot.jpg

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