Syncing problems when using multiple iPods on the same computer?

I own three iPods. An 8GB nano, a 16GB touch, and a 64GB touch.
iTunes seems to have no problems with the nano, but it seems to have issues from time to time with the two touch iPods. "Syncing" sometimes becomes "screwing up" in the form of deleting content that I have purchased.
My latest attempt to transfer a purchase (Toy Story 3) from my 64GB touch resulted in a "sync" which has basically corrupted my media libraries. I can see on iTunes that the media is still on my iPod, and even play it within iTunes from my iPod; when I disconnect my iPod from my computer and attempt to access the same media on the iPod by itself, both my music and my video libraries are showing up blank.
Has anyone else had the same problem?
NOTE: My 64GB iPod touch is not the latest version; it doesn't have the HD camera, but it does have the mic input. My 16GB touch is even older, having neither the camera nor the mic. The 16GB touch is an even bigger mess, with app icons frequently appearing as big grey blocks instead of the pictures they're supposed to be.
I like my 3 iPods. I like iTunes. I like Apple.
I just don't like it when things stop working the way they're supposed to.

Welcome, Brandon, to the Apple Discussions!
The answer to your question should be found here:
And if at some time in the future you decide you'd like to use an iPod on more than one computer, have a look at:

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