In order to fix this issue, you need to patch setDNS.pl file on your server. This file resides in C:\Program files\ensim\Webppliance\base\services\winvirtualhosting.
Please comment (add # in front of this line) the $IP = $addrs; line in setDNS.pl file and insert the following code below this line
After this all new sites in Appliance control panel would be added with IP address defined in Appliance network settings.
Note: This issue has been resolved in Webppliance Pro for windows 3.6 version.