If you use WPAD to distribute proxy settings to your users, then be carefull that 2003R2 and 2008 DNS does not place those DNS queries onto a black list. You need to prevent that by configuring your DNS server. This is done from the command line thus:
dnscmd /config /enableglobalqueryblocklist 0
Since this is an enable command, the zero means 'off' and a 1 means 'on'.
For further info see: