If you don't need the older version of Toad any longer, uninstall it from the Add/Remove Programs list, and it should stop this from happening.
The .sql extension (or the file extension being saved in Toad) is associated in Windows to an .exe file that is not Toad for SAP 3.1, but the older version.
To change this, find the file you saved in Windows Explorer, and then right-click it and choose 'Open With | Choose Default Program'
From here, click the 'Browse' button, and find the Toad.exe file from your v3.1 installation folder.
That should then associate that file extension of your new file with the v3.1 version of Toad.