I can confirm that. When I forget to stop the recording before I turn the mixer off (Sonar will not recognize the file), I use "FormatFactory", and convert my unusable file right into WAW file again in CD quality.
I had the same problem. What helped me was format the SD card in my Panasonic Camera (in my PC it did not help). After inserting card in the camera it suggested to format the media card. ...and at works like before. Later I just deleted the extra folders the camera created after formatting (SD 32GB, Class 10).