HELP!  iPod music skipping problem

Hi there! I am posting so I can get feedback on how I can better organize my music. First off, let me describe a problem that I am having on my iPod that I think is related to my iTunes library.
- While using my iPod with Click Wheel, I have (for example the Black Eyed Peas)10 songs, and it skips over a bunch of them except maybe one or two. Now, when I use iTunes all of the 10 BEP songs are the library and I can play them on my PC. I don't understand why they play on the computer but not on my player.
I think it has something to do with the way I have my music organized. Here's how I generally do it:
- In the Windows My Music folder, I seperate each artist by their name. In this folder I have each album separated. When I add a new album or artist into itunes, I keep the My Music/Artist folder open and have iTunes open behind it so I have the screens split. I then drag the songs I want into the iTunes library and they show up.
However, as I mentioned before I have songs on my iPod that skip even though the "appear" on the screen, they just can't find the song so it flashes to the next song etc.
Is there something that I am doing majorly wrong? What does the iTunes folder in the My Music folder do.
Should I be better organizing my songs? Also it seems I have a ton of duplicates!
Please help!

Other can be Album Artwork, Notes, Contacts, Firmware etc. or (and this doesn't apply to the iPod Touch or iPhone which don't have the option to enabled for disk use), files that are on there if you are using the iPod as a removable storage device. If you feel that Other is being incorrectly reported then try restoring your iPod. Restoring will erase the iPod's hard drive, reload the software and put it back to default settings. Once the restore is complete follow the on screen instructions to name the iPod and automatically sync your songs and videos onto the fresh installation. Press Done and the iPod will appear in iTunes and start to sync. If you want to update manually or using selected playlists uncheck the box beside the sync automatically instruction and press Done, it will default to manual mode and you can choose whatever setting you like: Restoring iPod to factory settings with iTunes 7

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