ITunes "losing" music--only finds it if I double-click on it

Recently I copied my iTunes music library on to my Time Capsule using the instructions here (http://support.apple.com/kb/HT1449) because I'm running out of space on my internal hard drive. (I haven't deleted the original files yet, since, as you'll see, it's not working well.)
Now, when I sync my iPhone, I get a message saying that some tracks were not copied to the iPhone because iTunes couldn't find them. (They're still on the iPhone, however.)
Also, when I go to these tracks in the Music window in iTunes, there is a little exclamation point on the left next to them. When I double-click on them, however, they play fine (so they exist). If the following track has an exclamation point next to it, however, iTunes doesn't play that track but moves to the next track without an exclamation point. It will only play it if I double-click on it.
The "missing" tracks are a mixture of whole albums and random tracks from other albums. I can't see any pattern to them. They are all tracks that are also in my iPhone, but not all the tracks on the iPhone have this problem.
Any suggestions?

The app is not gone, it is impossible to remove it from the device.
Check all home screens and folders.
If you are unable to find it, Settings > General > Reset > Reset Home Screen Layout.
As a last resort, restore from backup.

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