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You need to make sure there are no 'gaps' in your shipping rates. To look at your settings, on the far right side of the blue bar click on the gear-shaped button and go to Settings > Website Settings > Shipping, and click to Configure your shipping methods.

Check the box for the method you want to work with and click to Edit. Scroll down until you see the table with your From and To numbers and the Rates. In cases where your shipping method is based on Amount (the total dollar amount of the order), you need to make sure that the first line of your rates starts with 0.01 in the From column, and the From amount in the second row needs to be one penny higher than the To amount in row one. The 'gaps' are when you leave open amounts that do not cover every possible amount in your From and To range.

Here is an example of how to NOT set it up. The 'gaps' occur when you go from whole dollar amounts from one rate line to the next, so in this case, and order amount of $10.01 to $10.99 would not be charged shipping at all, since the first line only goes up to $10.00 even and the next line starts at $11.00.

For a good example of how to do it correctly, please click here and look at the Domestic Shipping section: How to Set Up Shipping Methods.