Steven Zahm@ John
I just searched the UAM code for core WP functions of add_cap(), remove_cap(), add_role() and remove_role() which would be used to add remove roles and capabilities. Unless custom code instead of the WP API is being used, I do not see UAM being able to remove custom roles and capabilities. I also activated on my test site and insofar as I can tell there are no issues.
The only thing I saw glancing thru its settings was an option to reset UAM back to its defaults. Did you by chance use this feature? If you did, maybe there might be something in it that does something to custom roles and capabilities. I would have to dig much deeper. But, before I do, I like to know if you used it or not. Because if you did not, then there’s really no reason to deep dive into its code.