I was having basically the same problem. Here's what I found on it:
A very common mistake made by most users is to simply try and move their entire iTunes Music folder to a new location and update the iTunes Music folder path in iTunes’ preferences. In some cases this may work, but in reality you will risk iTunes losing track of some or all of your music files in the process.
The reason for this is that iTunes stores the entire full path to each music file in its library database. If you move that file somewhere else, then iTunes won’t be able to find it, and the result will be a broken link to that file, shown as an exclamation mark in iTunes immediately to the left of the track listing. If you try to select a track with a broken link, iTunes will notify you that it cannot find the file, and provide an opportunity to locate it yourself.
Selecting “Yes” will allow you to browse for the file, and iTunes will link the current entry to that specific file. This can be a viable solution for a few broken links, but you can well imagine that this could become very tedious if you had hundreds or even thousands of files in this state.
Should you find yourself in this situation, the simplest solution is generally just to move your iTunes Music folder back to its original location. iTunes still has the complete path to each file in its database, so if you put the actual files back, it should have no problem finding them again.
Note that users who have a completely “Managed” library configuration may be able to get away with using this method to move their library, however it is still not the recommended solution. The reason this method will work in this case is because iTunes will actually look for any missing tracks in their default location under the iTunes Music folder path before deciding that the links are broken. So, if your tracks are organized in the way that iTunes expects to see them, then it will be able to locate them in the new location. However, this solution is rarely completely reliable simply because it is not uncommon for users with large libraries to have a few referenced files due to changes to iTunes preference settings or even inconsistent behavior with older versions of iTunes.
I didn't write this up though, I found all the info here:
http://www.ilounge.com/index.php/articles/comments/moving-your-itunes-library-to -a-new-hard-drive
Now I just have to spend another 7 hours moving my 500 gigs back to where they were, then another 7 moving them back here yet again!