If some FW solution is implemented, your scanner might not have any answer from your Linux-box. For example, if your 53 port is closed, either the scanner will give
or it may also mean you don't have any DNS filled on your ethernet card configuration on your Windows client.
I guess that each interface on the Linux machine is on a different VLAN (or network ayp) ?
Could you try to do another scan test with Nmap ? (
http://www.nmap.org/download) ?
Just to know more, you may have a look a the manual which describes how scanners do to get the information, especially also for Nmap (
http://nmap.org/nmap_doc.html).
Hope it helped... Keep me alive about this please.