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.
Despite your worries I tried putting one A4988 instead of the DRV (tried Z and X axis) and it didn't help. Exactly the same thing was happening as before.
So I'm starting to fear that arduino or RAMPS is faulty...
I have no problem ordering another one, but I'd like to test which one is faulty. Well, I don't think that the software is wrong, or all 6 motors are the problem. But I might take a look at the software once more, deeply.