I'm using PETG, the thickness of the filament is 1.75mm, in MakerBot there is a setting for "Layer Height", the default is 0.1mm, I've had lots of messed up prints with this material and I'm thinking it could be this setting that needs adjustment.
What layer thickness should be used?
Unlike PLA, PETG does not like to be "squidged" down, it likes to be laid down. If you use too small a layer height, there is the danger of the filament sticking to the nozzle, rather than the bed (or filament already laid down). Try using a larger layer height -- between 0.2mm and 0.3mm, if you have a 0.4mm nozzle.