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?