I have discovered that some ship designs will break the workshop uploader and you have to restart c++ to fix it. Until it is fixed you can't upload ships.
I am not sure why certain ships cause a problem, but my theory is that it is caused by starting a design from a previously downloaded design. I start most of my ship designs from a hull and not the start cube. If it is a game hull, no problem. Occasionally, I will start with a design I downloaded from the workshop. I completely change the design, deleting and adding parts, to the point that it is unrecognizable from the original. If I try to upload this ship to the Workshop, it seems to screw the pooch.
I have not tested this theory enough to be certain I am correct. I would be interested to hear if anyone has uploaded an altered ship previously downloaded from the workshop.
I hope this is not too far off topic, since it involves ship design. It is not my intention to hijack the thread.