Try running Process Explorer as an Administror
Yes, that was my problem (how embarrassing). So that is the issue. If you run while logged in, it runs at normal IO priority. If you have it set to run "whether logged in or not", it runs at low IO priority.
So that is a good trick for people to use if they want to use low IO priority until the feature is available. The only downside to using "whether logged in or not" is that you don't actually see the myDefrag GUI so it can't see the nice disk layout as it changes.
Thanks you two for your help and suggestions.