I found this thread through a search for the same problem I was getting a while ago, and after I found the solution, I came back to post it for anyone else who needs to fix their domain.
The problem is that sometimes when DirectAdmin is installed, some server hosts set the main domain to the domain that you entered in your registration. To allow you to use the domain as a regular user would, do the following:
1. Log in as an administrator (eg admin).
2. Make sure you are in the Admin Level. Click on DNS Administration under Admin Tools.
3. Tick the checkbox next to the main domain and then click the delete button to delete the domain.
4. Log out, then log in as the user you want the domain assigned to.
5. If you are an administrator or reseller, make sure you are on the User Level.
6. Click Domain Setup and re-add the domain.
You should now be able to use this domain just like any other domain in DirectAdmin.
These steps worked for me, I hope they help someone else.