Pretty hard to put this in brief into the subject 

I use s3sync to backup a server backup created by rsync to S3. This works quite fine, except for one folder: My IMAP-Folder. There are several accounts on the server and it happens only to mine, everything get's removed first and newly created afterwards, even if it hasn't changed for months.

As there are other IMAP-Accounts that are not affected I think this is an issue related to Apples Mail.app (running Mail 3.1 on Leopard 10.5.1). As my IMAP-Folder is about 5GB this is a quite expensive task if done on a regular basis. Currently I exclude my IMAP-Folder but is there any way to make it sync correctly? I don't think this is related to the issue but I use EU buckets.

Matt