If you have two or more versions of SQL Server installed in your machine, most of the time, when you open a .sql file by double-clicking on it, it gets opened with older version of SQL Server. This happens because of the registry-entry registered with the registry. If you are using latest operating systems like Windows 8, then it can be simply changed by accessing Control Panel -> Default Programs -> Set Associations. It allows you to set the application for .sql extension, you can either pick one from the list or browse for ssms.exe.
If the 5 Operating System is different and you have no way of setting it, you can try changing the registry entry and see. Not sure whether this is the right way of setting it but it worked for me. If you have to do it, test it in an environment configured for testing before applying it to production environment.'
If you navigate through registry (you can open it via regedit.exe), HKEY_CLASSES_ROOT has a node for .sql.
As you see, default is set to ssms.sql.12.0. If you scroll down through nodes, you will see this node and how it is registered.
Now if you want to get your .sql opened using a different version, find a relevant node (like ssms.sql.12.0, ssms.sql.11.0) and set it with .sql.
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