@ian.hilton: Grab the latest gfx2gf and see if that works for you:
http://www.ledseq.com/downloads/gfx2gf.zip
It now asks you if you want to use nearest neighbor on launch, and you have to answer Y or N. It will also ask if you want to crop if your source is not square.
NOTE: I had to update my copy of FFMPEG (dated 2013) for nearest neighbor to look correct. There were subtle inaccuracies in my old copy.