This is a bug, sometimes running Steve Easton's cache cleaner then republishing all files will synch up the files properly but not always. I'm not sure but it seems to happen more on some hosting company's servers than others so I can't help but wonder if it might have something to do with the GMT offset. Since I have one server I know doesn't have the GMT offset configued correctly and there is an issue with files showing confliced when they are not. They also show up as "newer" on the server if I am working in Dreamweaver instead of Expression Web.
Sorry I can't be of more help.
Cheryl D Wise MS MVP Expression Instructor: starttoweb.com