@stotman
I did something similar with my statistics course and there's a lot of set up and coordination needed. It's easy to miss a step in the process.
I do not see the "Complete All Items" at the top of the module header. That makes me wonder if you have the modules properly configured like you think you do.

You don't have a screenshot of the Edit Module Settings for the 01-01 Check-in Challenge module to confirm, but that is where I would start. If there are no requirements, or it's set to "view the item" instead of "score at least", then what you're describing could happen. The "view the item" is the default and there are times I've missed changing it for some items since the process is tedious and highly repetitive.
After fixing things, you will probably need to relock the module. It sounds like you're on top of things, but in case someone else needs more information, they may check out How do I add requirements to a module? in the Canvas Instructor Guide.