The file option in the Preferences is for setting the creator type for each of the file types. If you set jpg settings to Photoshop, all jpgs captured by Snapz Pro X 2 will automatically open in Photoshop when you double click on them.
To set the file type for the image being captured, invoke Snapz Pro X 2 (command shift 3 by default) and click on the button of the capture tool you want to use. Then set the file type in the File type popup menu.
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