As best as I can tell, the Migration Assistant only looks to the default location for resources to copy, if you have your resource folders saved to a different location it won't copy over stuff like custom materials.
When selecting to use the migration assistant, it should ask for the folder location of the prior version resources so that it looks to and pulls from the actual folders you are using and not just looking to the default location.
Updating from 8 to 9, I now have to go through and manually move all of my custom materials folders. :'(