The problem is when MPS creates a new site, the Search Service Account does not get assigned rights to the site; therefore, when you perform a full web crawl, it cannot crawl the site. Hence, search is broken. I can manually fix this problem and then searches start to work. This only happens when you create the site from MPS. If I use the STSADM command, then the service account is assigned rights and search works. I have confirmed the rights on the WSS 3.0 server, WSS Farm, and SQL Database. I have also confirmed "Execute As" in the Deployment Tool and tried re-initializing. When we discovered the problem, we were running RU 7 and have since upgraded to RU 9, but no difference.

MPS ?SP 2010 "FAQ" (mainly useful links): http://wssv4faq.mindsharp.com/default.aspx WSS3/MOSS FAQ (FAQ and Links) http://wssv3faq.mindsharp.com/default.aspx Both also have links to extensive book lists and to (free) on-line chapters

Thank Mike, I figured out the problem. The ServiceAccountDirectoryPath had a typo, it was pointing to an invalid OU.