I got a response from the company about my problem. I have copied and pasted it below:
We recommend that when placing the USB cord into the machine, that it is placed in carefully to prevent any of the prongs from becoming damaged. If you are experiencing a problem with the cord, please contact your authorized Janome dealer for additional assistance.
We appreciate your interest in Janome America, Inc.
Well I thought I would just ram it in from below, above, or from a side with enough force to move the blasted machine (which is in excess of 50 pounds). What a help. I really can’t believe it. Bury your head in the sand.