How to have my iPad use Win 2008 server's internet connection?
It sounds like a dns issue to me.  You'll want to have an internal dns server that knows to route *.example.com to your server's internal address and forward everything else to a public dns server like 8.8.8.8, and make sure your dhcp service hands out this dns server.

It could also be an ipv6 issue, as Apple products are configured to very strongly prefer ipv6 whenever they can.  If you have partial ipv6 support somewhere on your network (very possible to have without even knowning) it could be confusing the iPad.