So strange as this sounds, it appears MyDefrag is causing huge amounts of fragmentation on my volumes?
MyDefrag keeps a list of files that were unmovable on the previous run (the "MyDefrag.dat" file). It will test if all these files are still unmovable just after analyzing a disk by trying to move the first cluster of each file. If successful then the file is now movable. The test will fragment the files, because only the first cluster is moved. In the next version of MyDefrag it will move the first 50 clusters, so files smaller than 50 clusters will no longer get fragmented by "Analyze Only".