I have a few ideas as to what may be happening. First is build plate calibration. Try raising the height of the extruded slightly. It's a difficult balance to get a stable first layer that is not to tight to avoid the extruder bumping the print. Also make sure that corners are calibrated well. With a multi part print, the head may be hitting in one of the corners. Next look at your filament placement. Is the filament causing too much drag while moving on the x/y axis? The last is mechanical. I had terrible skipping issues when I first got my printer. The cause was debris/flashing binding up the sliders on the side rails. I had to remove the sliders, and clean them up with a small blade to remove flashing and allow the belt to slid through it freely. This is fairly involved because you need to disconnect the extruder rail before you can snap the slider off the rail. Hopefully you are now able to access the M3D forum now. They have good instructions for removing the rails.