When I use "Force.com->Synchronize With Server", the synchronize view shows some files as having outbound changes, when no changes exist. For example:
Each individual file difference shown here is a file for which no diff exists. When this happens, the icon is always a grey "outbound change" arrow. Double clicking to open the file diff shows no diffs of any kind; enabling/disabling the "Ignore White Space" option makes to difference. Right-clicking and choosing 'Apply Server to Project' pulls a fresh copy of the file, but the file still shows as a diff in synchronize view (even after running a fresh "Synchronize with Server"). Right-clicking and choosing 'Apply Project to Server' will save the file to the server (per the status message), but the again, the file still shows as a diff in synchronize view (even after running a fresh "Synchronize with Server").
These aren't the only email templates/objects/workflows in the org; there are plenty of items that are correctly synced and showing no differences. But once an item starts showing this behavior, it continues to do so.
I am currently using Force.com IDE v 126.96.36.199310181333 on Eclipse Juno SR2 (build 20130225-0426) on Mac OS X 10.7.5, but I have seen the behavior in other versions; I was using IDE v 28 on Eclipse Indigo previously and had the same issue. Is this a known issue? An Eclipse bug? Anyone have a fix or workaround?