I had the same thing happen to me when I joined Coinbase a few months ago, but they eventually processed the transactions at my original purchase price after emailing and posting on here. The price had gone up around $30/BTC during that time. If you search the forums, you'll discover this is pretty common, and they normally right their wrongs.

It's odd they didn't process the transactions at the original purchase price for you or even mention that as an option in their email responses. Their customer service has always been shit, but it is a nice service to use once you're at Level 2 and can buy and sell instantly.