MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
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Hard to say without seeing a photo or video, but what you describe usually points to the distance between nozzle and heatbed being too big. You might want to try raising the bed and thus decrease the distance between nozzle and heatbed. Also, you might want to try lowering the print speed. Different materials behave differently, so it's entirely possible that one brand of PLA sticks perfectly, while another one doesn't.