Are you listing in a Media category? eBay's efforts to block the abuse of MM can be quite crude, and can interfere with valid uses of MM.
One simple workaround would be to offer generic "Economy" shipping in your listing, with a flat postage cost based on the MM postage rate for your package weight.
You would probably not be able to purchase a MM label through eBay either, but you can purchase it through other online postage sellers such as PayPal.com or at your Post Office (price will be the same as through eBay).
