Teams that use worksets and link multiple Revit models started enduring this message a little over a year ago, around the release of 2008 methinks.
Autodesk finally pinned it 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.
If this seems vaguely familiar, Dwayne Lindsey posted about the newly minted Known Issue at Autodesk on his Blog Revit Arch-Center. I'm reposting because I read and responded to a question at AUGI and a couple clients were bumping into it recently. I thought why not echo it again...again?
If the dwg file is reloaded into the linked model or if the linked model is opened and saved the issue should not generate the message until the dwg file is altered again. If the file is NOT a "Link" then it wouldn't generate the message either. So that might be an argument to not listen to my normal advice to use the Link option with DWG files. Make rules and then break them is my "motto" 8-).
Proper credit to the guy I first heard nail it down, John Vogt with HOK St. Louis. John 'splained it to me at the HOK Cad Work Session I attended back in May. Sure enough he was correct! You are the MAN John! Cheers! I'll buy you a beverage next time around!
[I stole the image from Dwayne's post because I can't recreate the error in the latest build of Revit 20080602-1900, thanks Dwayne!]
[Amended: Andre Carvalho added this suggestion in a thread at AUGI:
The way I found it works nice, is avoiding to link the DWG that someone is still working. Instead of that, I first create a blank CAD file, XREF the DWG that someone is working and save in another folder. This new DWG will be the file I will bring into Revit. Because it has an XREF from the original file, I still can see the changes made in it when I open Revit, but because no one is actually opening it, working on it or saving the DWG I've created, I never get that message anymore...]