Mysterious version conflicts on creating project

When I create a project and pull in files from the server, certain files (BPLs and DTLs) aren't synchronized, and when I try to sync them (without making any changes) I get a Resolve Version Conflict screen, with differences between the local copy and server copy. Sometimes the Parameters are in different places,  or the Storage will be on top of one and on the bottom of the other, and sometimes the server copy will flat out have lines that aren't in the local copy at all. But in all cases, the local copy is correct, and if I look at the server file via Studio it always matches the local copy in Atelier, not what Atelier "thinks" is the server copy.

Have you seen this happen, and if so, what's going on?