If that doesn't work, you may have to mess around with the database a bit to fix it. I had the same problem with 0.6.1 DR2, but after messing around with the DB ,I was able to fix it. It was over a month ago, or I'd try to post everything I did...
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.
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