As previously reported, some users are experiencing a problem in which the Dock does not display its contents properly, with items sometimes disappearing. Previously covered fixes include recreating the user account and removing a series of Dock preference files.
Suspicion that the problem had to do with some of the .Mac/.Me syncing features later arose: applications that were synced through these services were those afflicted by the problem. As such, new fixes for this problem include resetting the sync data and removing some proxy settings.
Reset the Sync data In the MobileMe system preferences, go to the "Sync" tab and click the "Advanced" button down at the bottom of the window. In the resulting drop-down window click the "Reset Sync Data" button and follow the instructions to reset the sync data. NOTE: If multiple computers are used, be sure to know which computer has the most updated versions of the sync data on it, and reset the data to copy all information from that source.
Remove proxy settings, specifically PAC files In the "Network" system preferences, select the network adaptor being used and click the "Advanced" button down at the bottom of the window. In the resulting drop-down window select the "Proxies" tab and remove any URL that points to a PAC file. If "Manually" is selected as the configuration option for proxies, at the bottom of the protocol list uncheck the "Automatic Proxy Configuration", and optionally remove any PAC file URLs in the "Proxy Configuration File" data field.