Hi Chris,

> Anyone else help me identify the issue? Thanks.

Have you tried with a minimal org configuration?  I tried and cannot
reproduce the problem.  That suggests something else in your org
configuration as the culprit.

I have attached your example TODO (habit) as henderson-habit.org.
Update the paths as appropriate in the attached minimal-org.el, then
star emacs with it and see what happens for you.

emacs -Q -l minimal-org.el

After issuing M-x org-agenda a, I get an agenda with a consistency graph.

Best,
Josiah