If you are talking about the tag <unknow guild> in a character when creating a new guild is a database issue, usually fixed zonning. If you are talking about those NPC guys with <unknow guild> tag that are untargetables is a code issue in Cavedude's serverpack.
How to fix the code in second one is not public yet afaik, check
http://eqemu.sesmar.net/forum for more info.