Two tests that may help:
First, test your renumbering settings on a different set of Mp3 files from a different source, but using the renumbering settings that you have shown us in your screen shot. I suggest testing music files ripped from a CD, if you have any such. My guess is that renumbering will work as expected.
Second, please see this Help page for file checking tools: How to check files for errors?
Use a utility like Mp3diags to check some of the Mp3 files that won't renumber and tell us what (if any) anomalies are reported. A screen shot of the Mp3diags results would be helpful.
Also, in the future please add the Track column to your Mp3tag screen shots (it is missing above). That is important because the Auto-numbering Wizard fills only the Track and DiscNumber tags.