As far as I can tell, the restriction your shipper was describing is only in effect for 'farm equipment.' From the official Department of Agriculture Foot & Mouth Disease website, I found the following FAQs:
Q. What are the current requirements for the importation of used farm equipment from a FMD affected country?
A. Effective April 13, 2001, used farm equipment presented for entry into the United States requires an original certificate declaring that the used equipment has been steam cleaned and is free from all dirt and other organic matter for entry into the United States. If the shipment is not accompanied by this certificate, the shipment will be refused entry.
Q. What are the requirements for the importation of a vehicle, other than used farm equipment?
A. All motorized equipment will be inspected at the port of entry. New, used, and personally owned motorized equipment must be free of all soil, manure, and organic matter. Dirty motorized equipment must be cleaned before release.
Q. What are the requirements for used tires?
A. Tires, new or used, must be clean and free of any soil, manure, and any organic matter prior to release.
So ensure your bike has been cleaned, including the tires, and is free of soil, manure and organic matter before it goes in the box, and you should have no troubles at the USA end.
Anybody else have any different experience in the past year, please chime in!
"It matters not what goal you seek
Its secret here reposes:
You've got to dig from week to week
To get Results or Roses."
'One world, two wheels'