Sounds like something is not right: are you sure you are looking at the same database both times?
I'd check the db name in the config.php to be sure. And also make sure that the database user name is correct and has the proper privileges in the db as it should.
Consider adding the Adminer plugin to check the database from inside Moodle as the moodle database user.
As a sanity check, on the database run the query
SELECT COUNT(id) from mdl_user WHERE deleted = 0;it should return exactly one more (because it includes 'guest') than the number of active users you see in at the top of the Browse list of users page.
When you manually create a user or upload them, it should immediately add them to the database. It doesn't wait for the email to go out or the user to be confirmed or anything.