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.
That explains all... the fact is every machine and slicing app work differently and some cannot deal with more complex designs. The Revolver has worked well and with no issues for most people but the few who do have issues are running the less known machines and apps. The mainstream machines and apps usually cost more but are also more refined...
So my suggestion is to try repositioning (rotating) the file in your slicer before slicing it so it will read the file differently and change the toolpath. That may help it overcome whatever it cannot deal with.
Failing that try scaling "all parts" up uniformly 3 - 5 %. This will have a similar effect so the slicing app handles it differently and also larger makes everything a little less detailed so it becomes easier to deal with.
I hope this helps...