I have been getting the exact same issue with both my mod characters (uninstalled, reinstalled and fresh downloads of both NT and NTT) I am making and others I have downloaded, even though I thought it was because one of my characters was pre-9921, as he worked with 9900. If you ask if it occurs with game play changing mods, it does not, as I am able to play the Hardmode mod just fine.
Theory: Maybe it's related to the save files where you're Nuclear Throne progress is saved in the users/name/appdata/local, testing this.
Edit: Definitely something to do with save files. I removed my whole nuclearthrone folder in that directory and my mod character worked perfectly fine, though I didn't check multiple times in a row to see if a write to the save messes it all up.