Well, your issue is at least isolated whereas most ecommerce puzzles can be many things. Ask yourself a few questions:
- Is shipping only calculated on final checkout? Maybe they're just stepping through to see how much shipping is. Check your competitor shipping methods and prices.
- Does the user have to create an account to check out?
- Compare your checkout against other sites. Are you doing anything really cool, different, novel, unique on checkout? DON'T DO THAT. :-) Users have expectations, meet them.
- How is it organized? Billing info, shipping info, supplemental, credit card info?
- Design, has the form got good high contrast and is not using tiny labels or tiny text on important items?
- How many "non-web savvy" users have you pointed at the form? Gather up all the grandma's, uncle's, children, and as many other people that you can collect that have ZERO INTEREST in your topic to walk through the process. Don't talk to them, don't explain (if you have to explain, you are doing something wrong.) Listen to them. This is your "average user."
- (Stupid question, really) SSL cert working and in place, using the SSL icon provided by the CA?
- Payment methods: PayPal only, or anything else that requires the user to do "special things" when entering payment?
- Please don't tell me you're using CAPTCHA on checkout. :-)
There are probably lots more, but it's really rather simple, step outside what you think you know and listen. :-)