Hi Adam,
@Damian Culotta's suggestion would have been my first suggestion too. However, if there are no active Shipping Methods (either globally or for the Website in question), then, I'd look for a shipping extension buried within your site. While most shipping extension that would include this type of shipping functionality would add themselves into the Shipping Methods area, perhaps there's an extension that - for whatever reason - is not.
You can look through the main menu in your Magento admin of course. You can also go to System --> Configuration --> Advanced-Advanced, and click on the Disable Modules Output tab to open it up. This will list your modules/extensions. Generally speaking the ones that start with "Mage_" come with Magento off-the-shelf. So do the modules called "Cm_RedisSession" and "Phoenix_Moneybookers". If I were you, I'd be looking at what else you have installed in order to understand what else has been added, including any custom extensions that may have been created by your site developers.
Most extensions are labeled with the name of the developers, and the name of the extension (ex. JetRails_2FactorAuthentication). Certainly, if you find something labeled as a shipping extension, you may be able to either track it down in your Magento admin in order to adjust the settings, or track down the website of the extension developers, which may include support documentation.
If your shipping prices aren't coming from a Shipping Method or a Shipping Extension, then I'd imagine the most likely culprit is some other customization that's unlikely to be managed from the Magento admin.
PS - It sounds like you may have already checked for Shopping Cart Price Rules that may be a part of your shipping - such as for Free Shipping, but if not, I would check those too. Those would be under Promotions-->Shopping Cart Price Rules.
Best of luck!
