I really need to brush up on my SQL skills. I think this is happening from the inner joins between groups & grcategory since the inner join only includes records that have data in both (e.g. there is a group with that category) I have been unable to find were to change this, but see Krileon has resolved this issue on the forge for beta5:
forge.joomlapolis.com/issues/show/1228.
It sounds related to my issue of categories with no groups are not being displayed in the overview. If someone finds a fix, please let me know as I expect to be patient for beta5