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.
Which version are you printing? I'm really curious how this is happening, none of mine have done that at all. The V13 version (which I haven't uploaded yet, but am now printing with) should be better, I moved the brace arm further up, which should help, but I haven't had any tendency to flex at all.
What temperature and material are you using, and what infill percentage (and pattern) are you using? Which orientation did you use?