iTunes keeps screwing up my folder organization

I keep all my iTunes media on an external drive, because it's far too large to store on my internal hard drive. I changed my iTunes Media folder location to my external drive, but for some reason, iTunes sometimes screws this up and creates a new iTunes folder on my Mac's internal hard drive. While cleaning out my internal drive, I thought these were old back-ups and deleted them. When I started up iTunes again, I was told that the library could not be found.

So I had to recreate my library all over again. I have the "Keep iTunes Media folder organized" option checked so that everything is kept organized. But now, this has screwed up the organization even further.

Here's what the file structure should be:

/Volumes/External HD/iTunes/iTunes Media/Movies

But now, my movies are split into multiple folders:

/Volumes/External HD/iTunes/iTunes Media/Movies

and

/Volumes/External HD/iTunes/Movies

and

/Volumes/External HD/Movies


I've tried twice now to straighten this out, and twice iTunes has split my movies between three folders. I've also got multiple listings for the same file, sometimes with slightly different metadata. Does anyone have any suggestions on how to fix this mess?