I've had something like that happen to me some time ago.
The domain in my case did also have it's own DNS settings.
Because I could not add the domain anymore (error: the domain is allready used by.....) I could also not remove it as it did now show in ISPconfig.
In my case the "bad" domain was causing Bind not to work anymore!
I had to digg deep into the ISPconfig DB, and fix it that way!
The tables are all linked together in the ISPconfig database, so make 100% sure that you know what you are doing! (make a backup!!!
Here is the link to my problem: http://www.howtoforge.com/forums/showthread.php?t=11798