I have 3 shipping methods, Flat Rate for U.S. only, Free Shipping for U.S. only and a Table Rate for International select countries. When in the cart if you enter an international location the Flat Rate and Free shipping options do not display as I have set "Show Method if Not Applicable" to No. However, if placing an order to be shipped to a U.S. location the International option (table rate) still displays even though I have set "Show Method if Not Applicable" to No and United States is not selected in the "Ship to Specific Countries" list.
After poking around a bit I found the issue! I had set "Show Method if Not Applicable" to No in the Default Config but not in the Main Website configuration. So if you are having similar issues with any of multiple shipping methods showing or not showing, review your selections in the Main Website Configuration to make sure you have same shipping rules chosen as in the Default Config. (Use drop down menu of Current Configuration Scope: in top left hand corner to look at the Main Website view).