That "DeepScan=0" setting is correctly set in the INI file. What's happening is when loading Recuva and using the Wizard it does not show the Deep Scan box ticked even if it has already automatically enabled it without me knowing about it.
I think it's automatically enabling Deep Scan once it has finished scanning with the Wizard and opens the file list, and subsequent uses of the program will then have it automatically enabled on program startup, but since it's doing all this without my knowledge I'm not entirely sure if it's happening where I think it is.