nmr,
thanks for your suggestion. So finally had a chance to go back and do some more testing. Using your suggestion, I realized that I was missing a custom capability for my custom taxonomy. Not sure what happened to it as everything was working before my update to 5.1.1 but anyway, I found the one missing cap that would allow for my custom taxonomies to show up for the admin, added it and now it works. Problem solved!
Thanks for the suggestion.