When I upload the file, all I get in the .htaccess file is:
#### CC BEGIN WEBSITE ACCESS MANAGER ####

#### CC END WEBSITE ACCESS MANAGER ####

The password file uploads fine each time. I have tried deleting the old ones, re-imported the users, etc and nothing has worked so far. Even upgraded from 4.0 to 5.0 and that didn't change anything. I have uploaded to the same site before and have not changed any of the settings.

Dale
Sounds like you forgot to enable permissions for the folder and users in WAM and are uploading and an empty user file.
Did this myself a few times with the same result
Cayucostom

All users have been given permission. The password file has them all listed and is correct. It looks like it always has.

Check to see if you have an expiration date set to any users. If the date is wrong, that will cause the issue you are describing.

Found the issue. Under "Tools" and then "Show Protection Status", the protected directory was listed 4 times. I deleted 3 of the 4 instances of this and left just 1. When I re-uploaded the file, it was correct. Don't know why the exact same directory was listed 4 times though.