MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
I've hit this a number of times. It's ultimately a heat/cooling problem. Put a random post slightly taller than your print about an inch away from the peak that's printing poorly. Your extruder will need to move away from the actual print to make it and give the plastic that extra few seconds to cool down properly. It should solve your problem.