When trying to save a Web Intelligence document in the "Web" mode (not the java "Rich Internet Application" mode), users get a "Save As" window if another user was the last one to save the document. The user can simply select the same location and "overwrite" the existing report. They can also use the Rich Internet Application mode instead, since this does not have the same issue. After that, the same user can continue to save the report as usual, until another user saves it. The user has full control permissions to the document and to the folder.
This doesn't seem like it would be a big deal, but most of our users access reports using hyperlinks from other websites, which opens the document directly in the web mode; and they just make simple changes like selecting a different value in an input control. If the Save As window comes up, it takes them to their Favorites folder, and they usually don't know which public folder the report is stored in.