www.johntimney.com

You might be suffering from something called a Security only Crawl.

http://blogs.msdn.com/russmax/archive/2009/02/09/troubleshooting-security-only-crawl.aspx

One possible fix for this is to install the Feb 2009 MOSS Hotfix cummulative package.

http://support.microsoft.com/kb/967209/

Although, I've not suffered from this specific problem it can be a bit difficult to identify a root cause. Generally, security only crawls impact MOSS farms that make heavy reliance on Sharepoint groups and don't use AD groups, causing a ripple of unapplied ACL changes that Index has to force apply as it indexes.

As with any hotfix, especailly a cummulative one - test, test and then test again before you install this to live!