Cloned GitHub repos ask for a password, while originally created don't

My guess:

Your old repositories used SSH remotes ([email protected]: or ssh://[email protected]/ prefixes), which used public-key authentication. (In fact, the Github SSH server never asks for a password.)

Your new repositories use HTTP remotes (https://username@github.com/), which only support password-based HTTP Basic authentication and do not use your SSH keys.

Change your remote URLs to use SSH again. Use git remote set-url or edit .git/config to do this. Replace

https://username@github.com/username/repo.git

with just

[email protected]:username/repo.git

You can even have an entry in your ~/.gitconfig that tells git to translate remote URLs from HTTP or Git to SSH.

This way, if your repository is configured for a HTTP or Git remote, git will ignore that setting when pushing and will use SSH instead.

[url "[email protected]:"]
    pushInsteadOf = git://github.com/
    pushInsteadOf = https://github.com/

(An insteadOf = setting is also possible, to override both pulling and pushing.)