I'm using a Replicator 1 Dual and find that prints using the left extruder print 20mm to the left of those made with the right extruder. The distance between the extruders is 33mm, so there is a correction being applied somewhere, but it's not the right correction.
The right extruder is correctly centered. I do have the correct settings in Prefs->Machine and have selected the correct firmware in Tools->Firmware Configuration both for the Profile (Sailfish/Makerbot) and the Machine Profile (Rep 1 dual). I have no other problems printing with this set-up.
My rep 1 is running Sailfish 7.6. I have not tried any dual extrusions yet.
Any suggestions as to where to look?