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.
XYZ DV 1.0 is far from the worst 3D Printer :). You got an surprisingly good 3DP for that amount of money. Besides that, if any probs appear on the XYZ software, check your files with Meshmixer's inspector. If any errors are in the file, you'll know and be able to fix it. But its highly doubtful since the files are repaired at netfabbs online repairservice.
A possibility however is that XYZ's software does not agree with my designed wall thickness...
In that case, offsetting with meshmixer/meshlab(google it) could work, you'll just have to take a drill to the backplate's holes afterwards.