Take a look at this
Blog Post by Dwayne Lindsey. Autodesk finally pinned down the error causing it. The first person I heard nail this was John Vogt with HOK in St. Louis. He was spot on and I read Dwayne's post a week or two later...
It comes down to THIS:
If a linked RVT file contains a linked DWG (or other "CAD format") file, and the DWG file has changed on disk since the last time the linked RVT file was saved, then when the linked RVT file is loaded (as a link) the DWG file is reloaded which Revit interprets as a modification.
One way to avoid this entirely is to never import cad files into Revit
. Okay now that you've stopped laughing. Seriously, you could choose not to link certain files which means that Revit doesn't try to reload them when the project is loaded etc. Easier said than done I suppose. Better if Autodesk just traps the error and doesn't bother us?
Edit: Are you using build 20080602_1900 (found under Help menu > Product License and Information) In some testing tonight I was not able to recreate the error with this build.