Kbase Article of the Week: Mac OS X 10.3, iDisk: Local iDisk Sync Issues, Some Folders May Appear Empty »

Apple Support:

Every 72 hours after you start up or restart your computer, a routine maintenance task (or “cron job”) runs that can affect iDisk. If you have selected the “Create a local copy of your iDisk” option in .Mac preferences and cannot sync after your computer has been on for three or more days, download and install the Mac OS X 10.3.1 Update or later.

Similarly, if the Backup, Library, or Software folders of your iDisk appear to be empty, download and install the Mac OS X 10.3.1 Update or later.

It’s a tale as old as time: the .0 of any release brings weird bugs.