Since I don't have a support ticket in and I bdraco was nice enough to answer here, I'll see if I can adequately communicate the problem. His original ticket follows:
&Everytime I use my web host manager to add a new account it screws up my add on domains that I have set to my account. Any idea why this happens, and can you remove all the domains on my account and readd them for me since it says I don't have permission.&
When asked for an error message he replied with the following:
&&The subdomain, *********.net has been removed.
Sorry, you do not control the domain **********.net!&