Preupgradecheck Failure: Content database with modified database schemas

While recently running a preupgradecheck on a MOSS 2007 farm, I received the following scary error:

Failed : Content database with modified database schemas 
User modifications to the SharePoint content database, including but not limited to table schemas, index, stored procedures, are not supported and will cause upgrade to future versions of SharePoint to fail.The databases in the following list seem to have been modified from the original schema:
Data Source=SEVER;Initial Catalog=DB;Integrated Security=True;Enlist=False;Connect Timeout=15

My first thought was that someone must have been messing around with the database but I certainly don’t think any reasonable SharePoint developer or admin would make a change to the schema of a content database. After some hunting, I turned up this page. Buried at the very end is the following:

If you did not make any manual schema changes to the database, you can ignore this error and continue with the ugprade [sic]. This is a residual error from the upgrade process from SharePoint Portal Server 2003 to Office SharePoint Server 2007.

So, if you upgraded from SPS 2003 to MOSS 2007, you should expect to see this complaint from preupgradecheck. The upgrade to 2010 will work just fine. Now if I can just figure out where all those missing features came from….