It looks like the data being saved in raw is off by one pixel or line. This was caused by some pixels or lines being lost while saving the video which in turn makes the demosaic in the DNG viewer/editor software fail.
What version of camApp and, if it shows it in the util menu, what FPGA version?
As for recovering, there's a way but it's a bit involved and technical.
If your comfortable with a hex editor you can use The GIMP to open the raw file as type 'data' to find the offset needed then remove those bytes from the top of the file. In the options while opening the 'data' file you select greyscale-16bit, set the horizontal and vertical size to match what you shot, then use the offset entry to skip forward a few frames then offset until the image is lined up. Once you have that offset figured out, remove that many bytes from the top of the RAW file and retry running the script and viewing the result. If it still has artifacts, add or remove two bytes until it looks correct. If it looks extremely corrupt, remove only one byte.
A much better option is to save DNG directly using one of the newer software releases. DNG saving is far more reliable than the older RAW mode and gives the added benefit of saving some metadata such as the resolution, whiteballance, etc.
I hope this helps, let me know if you need further details.