<p>I run a high school 3D printer lab and we have several 5th generation MakerBot printers. On one of them I have considerable trouble with "thin" prints and filament slip warnings.</p>

<p>So far I've tried changing extruders and using different filament rolls with no luck. But, if I move the job and the extruder to a different printer it works.</p>

<p>I'd appreciate suggestions for how to sort this out. I would have expected the slipping problems to follow the extruder.</p>

Oh interesting. By slips, I take it you mean that the raw filament slips, not the print slips.
This will happen for a few reasons. First the tooth gear that grabs the plastic is either:
Worn out
Out of place
Not the correct distance from the guide wheel.
This is all part of the mechanism that the Smart Extruder attaches TO. Not the Smart Extruder itself. You might be able to fix this yourself, worst case you will need a replacement assembly from MakerBot.
I would look into online auction sites for the part
Another option is to try thicker filament. Which you might be able to custom order. So instead of 1.5, maybe get 1.8. I am not sure where you can buy off sizes.
From there this machine might just be getting jammed. It happens to some machines. This again points to the base of the X axis assembly.
Last which I would say is not likely as you have tried multiple extruders, you might have the nozzle becoming clogged. I often pop open my extruders
voids warranty
and clean them out. Also micro hand drills are a good option here.