The same has just happened to me :/
I just added a site in and since adding it all 20 other sites not point to the new one.
I also have now got some rather unhappy clients.
I have looked through all the conf files and they seem to be pointing to the correct places.
Had I knowen ISPConfig 126.96.36.199 is NOT stable I would have used the 2.* series -.-
Any help would be great please even though I feel it would be better to drop back to the more stable 2.* series