Setting all the vhosts to have an IP does not change anything. I tried splitting the IPs like they currently are, and I tried setting them all to the same. In both cases, they still all redirected.
Setting all the vhosts to * made all of them work, EXCEPT the currently functioning domain. The subdomains of that site worked, but the main domain did not. It redirected to the standard ISPConfig welcome screen - even though there is another index.html file in the root of their web folder. Where could it be looking for this, if its already been removed by the client?