Clearly iTunes cannot sync content that cannot be located, so you need to fix problem 2 first. Problem 1 might be a dodgy cable and/or fluff in the docking port leading to a flakey connection.
The "missing file" issue with exclamation marks happens if the file is no longer where iTunes expects to find it. Possible causes are that you or some third party tool has moved, renamed or deleted the file, one of its parent folders, or the drive it lives on has had a change of drive letter, or you've moved a non-portable library to a different path (see Make a split library portable for details). It is also possible that iTunes has changed from expecting the files to be in the pre-iTunes 9 layout to post-iTunes 9 layout, or vice-versa, and so is looking in slightly the wrong place, or that you've been too aggressive when deleting duplicates. See Getting iTunes & Windows Media Player to play nicely if you're trying to access your media with any other media players.
Select a track with an exclamation mark, use Ctrl-I to Get Info, then click No when asked to try to locate the track. Look on the file tab for the location that iTunes thinks the file should be. Now take a look around your hard drive(s). Hopefully you can locate the track in question. If a section of your library has simply been moved, a folder renamed, or a drive letter has changed, it should be possible to reverse the actions. If the difference between the two paths is an additional Music folder in one path then this is a layout issue. I can explain further if that is the case. If everything is where it is supposed to be try Repair security permissions for iTunes for Windows.
In some cases iTunes may be able to repair itself if you go through the same steps with Get Info, or when playing a track, but this time click Locate and browse to the lost track. It may then offer to attempt to automatically fix other broken links. Although it says something like "use the same location" I think it expects to find the tracks in the same artist & album layout they were in previously, with one systematic change to the path.
If another application like Windows Media Player has moved/renamed the files, or the library has been moved from OS X to Windows, then the chances are that subtle differences in naming strategies will make it hard to restore the media to the precise path that iTunes is expecting. In such cases, as long as the missing files can be found somewhere, you should be able to use my FindTracks script to reconnect them to iTunes. See this post for an explanation of how it works. It might need some tweaking if your media is in a non-standard layout.
If you want me to try to provide specific advice please post back the following details:
- The location of the media folder under Edit > Preferences > Advanced
- The location of a sample missing track shown under Get Info > File > Location that begins file://localhost/
- The true path to the file whose details you gave in 2
Note the addition of file://localhost/ (and the flipped direction of slashes in Windows) is normal for a file that isn't quite where iTunes is expecting to find it.
tt2
