Did a reset password and set a new password. Then, when trying to login with new password I got: "Your account has been disabled. You are not permitted to log in." Where should I start to look to resolve this?

First thing I'd check is the "Give access" field on the customer record.

I did @Dominic B and give access is checked

Not much else I can think of, aside of manually setting a password in the UI and checking the assigned website and roles are correctly set. I've had odd cases in the past where web/UI updates didn't work and the only way we could restore access was setting the password in the console.

@Dominic B Wierd, setting a password manually on the customer record worked. Any reason or way to resolve this so as to not have to do manually for each customer?

Not that I know of. I've found it just happens very occasionally with a very small percentage of customers. May be worth checking the script log for any clues, or seeing if you've got user events on customer records which might be erroring in the background.