I am having a similar problem. To me it seemed like it was printing the object on the same layer as the raft so the nozzle would rub against it and shake the whole build plate. Eventually it would say 'filament jam' and stop the print. I haven't found a solution yet, just been printing without a raft when I can.

Also:
Printer: Replicator 5th Gen
Software: Makerware 3.8
Firmware: unknown
Filament: Makerbot filament