Not sure if this is a bug or bad design by eBay.
When you switch the site to eBay Motors under the Advanced tab it deletes any shipping services already entered in the template.
I got an error message stating the shipping service was missing, but it was there before switching to eBay Motors as all my templates for the main USA eBay site have the correct shipping services.
A quick workaround is to create a separate set of templates for eBay Motors with the site already set to eBay Motors so its not deleted.