It's an artificial geographic restriction that Amazon have put in. Essentially the .com Amazon Kindle store is accessible to any Amazon customers worldwide (except for customers who's account has an address in a country that has its own Kindle store). Country specific Kindle stores, like Amazon.co.uk's Kindle store are only accessible to Amazon accounts that have an address in that country.
So, the Amazon.co.uk Kindle store is only accessible by UK devices, based on a UK Amazon account. The Amazon.com Kindle store is accessible to everyone worldwide who has a non-UK Amazon account. The same thing happens for the newly launched Amazon.de Kindle store, only users with German or Austrian addresses can use it. It's based on your account's home address/billing address, not on which website's account you use. You can apply to Amazon to have your Kindle account moved from .com to the country-specific site, if you created your account before your country's site was available, but you can't use two sites at the same time.
Presumably when more countries have their own Kindle store, they'll be locked out of the .com store, and other countries will be locked out of their country-specific store.