You’re right that Customize > Rules does not list the .mdc files in C:\Users\<you>\.cursor\rules. That is not something you misconfigured. Cursor only discovers .cursor/rules by walking up from the folder you opened. Home-level files are picked up only if that folder sits inside your user profile. If it does not, they stay off the Customize list and are not applied.
For rules that should apply everywhere, add them under Customize > Rules > User Rules. Those show in the list and apply across projects: Rules | Cursor Docs
Project-specific files can stay in <project>\.cursor\rules.
We’ve let the team know about loading the home-level folder globally and showing it in Customize. I’ll post here when I have an update.