It sounds like your pen-lift motor is failing. The only “expendable” component of the AxiDraw is the small, blue pen-lift servo motor. They do wear out over time but are inexpensive and straightforward to replace. For heavy duty applications — and this, with many thousands of segments qualifies — you may wish to keep a spare on hand. You can find them here:
You’ll need a small phillips screwdriver for the replacement.
There are some additional factors that can lead to the motor failing prematurely: For example, if you’re adding extra weight or pressure to the Z-stage, or if the pen lift stage does not slide freely up and down for other reasons, so check to see what the situation is.
On Rhino: We don’t have experience with it — you might look at what the SVG of the export document looks like.