I actually just had almost this exact same issue with my makerbot rep 2. After fiddling with the machine to no avail, I finally replaced the SD card I was using to transfer my .x3g files and the problem vanished. Could be you have a corrupted SD card on your hands.
I am using the latest MakerBot Desktop and im printing over Wi-Fi.
I’ve had the issue with several models. Sometimes they print fine, sometimes it fails. I’ve tried running models through meshmixers print preparation (including repairing) and cant see any impact on my results.
Depends on the speed. I had a similar issue in the past, where one pin on the carriage was broken. Maybe it is unlikely, but it´s also very easy to check
5th Gen: I had a glitch where the extruder was dragging on the build plate or raft hard enough to stop movement. It sounded like the machine was struggling so if your machine sounds like its moving smoothly it’s probably not your problem - just something to keep an ear out for.
I resolved the problem with firmware and desktop update AND going through a fresh leveling.
I have a similar problem and I believe that there are a problem with the connection between computer an printer. I’m using an usb cable. The printer don’t stores the file transferred from software, it has an small buffer , if the buffer gets empty without new data from computer the printer stops till new data comes… I recommend try to print loading the file to SD card