I had it happen last night on WHM 5.0.0
The customer said she tried changing the username, saw that it wouldn't work so deleted the account. Here is the exact account:
Yes, I tried to change the username. I realized that when I created the ******.com domain, I had put admin as the username, and that got translated into domain directory. There was an option in WHM that allows one to change usernames. When I tried it, it said that the feature was not available at this time. I then deleted the domain, and parked it at *****.com domain.
Well while she was parking the domain, I was removing the account from httpd.conf manually and trying to get apache restarted. Luckily I was sitting right at a terminal window when it happened.
For rthe posts above, I don't think it has been cured, I think it just hasn't happened again (yet).