Multiplying files on time Capsule

Months ago I uploaded my vast CD collection to my computer through Itunes. After a CD was done it would get transferred to my Time Capsule HD in order to free up space on my cpu and because this is primarily what a bought the TC for.
I had noticed over time that some particular artists were being duplicated, so I manually deleted them from my Itunes with the option to 'delete files'. One day I decided to delete all the music in my Itunes library and re-add it in order to add any files I had missed... This turned out to be disastrous!

My Itunes picked up 30 gb of music, the problem was most of it was duplicated of even quadruplicated. So to fix this, I went through my music, nearly 160 gb, and individually deleted as many copies as I could find. This wasn't the correct answer though. When my TC was takign on more space that Itunes claimed I had in music, I knew something was wrong. I looked into a folder that I recalled having many duplicates and there was the problem.

So i spent a day or two trying to clena up the folders. I deleted, directly from my TC, about 30 gb's of copies. I deleted everything on itunes, added the folders back, and somehow the 30 gb of free space was consumed with only <1 gb remaining. Does any one have any clue what is going on with itunes/time Capsule? Am I doing something wrong or is t the programming? Can I fix these problems? easily? Thank you all for your assistance!
SM