After some trial and error I was able to reliably print parts with nylon (618 from taulman 3D) on my MakerBot Cupcake.
I used the following temperature settings:
Heated build platform: 60°C
I had a lot of trouble getting the prints to stick to the platform. Here is what works for me: 3M blue painter's tape, topped with a thin layer of glue from an UHU stick. I enable the "raft" option for all prints. The raft adheres very well to the blue tape covered with glue, so well that I have to replace the tape for each print.
I use ReplicatorG 0037 to control the printer and the integrated Skeinforge 35 to produce the gcode. Here is my custom profile to print Taulman 618 Nylon: SF35-cupcake-HBP-nylon.tar.gz.
1. Heat the nozzle to 200C 2. Run Nylon filament through the extruder 3. With Nylon in the nozzle, reduce the temperature to 135C, and once there let it sit for a minute 4. Slowly but firmly work the filament out of the top of the extruder
This has worked very well for me a couple of times. Here is how the filament looks like when I take it out of the extruder (repeat steps 1-4 until it comes out clean):