I had this same problem and contacted MakerBot to see what they could tell me. Their advice was about right, but I had to tweak it to get it work properly.
First you need to make sure your firmware is up to date. The Bot comes standard with 1.0.1.18 and I believe and they are currently on 1.0.3.44. Just open the MakerBot desktop, select devices from the toolbar and then choose Update Firmware. (Devices>Update Firmware)
Second is the examining, cleaning and reattaching your smart extruder. I have tried doing this several ways, and it seems that there is only one way. First unload your filament and wait for the extruder to cool completely. Then power off your Bot. You can find this under Utilities. Next completely cut power to your Bot by flipping the switch on the back. Now that the Bot is off gently remove your smart extruder.
1. Examine the extruder and check out the pins on the back. Make sure they can be depressed and that the return to their original height. To the left of the pins is a silver, toothed, nut , make sure that it rotates freely. Also check out the cap nut on the front opposite the toothed one. Make sure that it is secure inside the extruder. If you see any problems with the extruder I would contact support and make sure to give them the SN for the extruder. If its functionally move on the cleaning.
2. Check the tip to see if you have any leftover material that has melted on. You'll want to remove it and possibly shine up the tip just a little. I would use a wire brush with thin but stiff bristles.
Once you think it is good and clean turn the power back on and wait for it to complete the start up process. Once its ready to go, reattach the extruder.
3. The attach process is under Utilities, (Utilities>System Tools>Attach Extruder). Start the attachment and then gently place the extruder back on. Make sure that the centering pin is aligned to the center of the nut, and that the toothed nut on the back of the extruder is completely attached the the corresponding toothed nut on the gantry.
Now try running your level build plate process. Even after running the assisted leveling I really haven't had a truly level surface. I think this might be because the plate for the build surface isn't a very sturdy/precise design. The best result I've had is when I used a gauge block and manually leveled the surface to the extruder. It took a lot longer but it seemed to work.
I hope this helps.