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'm not an expert, but my guess is that you need to change the fan settings. Try that, and if it doesn't work, just get over it. If only the top cube becomes warped, maybe it won't make as much of a difference.