Yeah I noticed this a few days ago and it's really annoying. So far I've converted 146 movies, TV shows and random videos to Zune format w/ 3rd party software (approx 40GB) . I own a Zune30 that has approx. 12GB of music on it that's staying where it is. So obviously, I'm not gonna put all the videos on my Zune. After I sync videos to the device, I archive those files on an ext HDD. So my folder I have the software monitoring rarely contains the same files as the device, so I've been getting thing deleted off my Zune that I don't want to be, of course.
As a work around, I mounted the ext drive and gave it a drive letter, so now I have to wade through 146 files that are organized for crap. I edit my video metadata so episodes of the same TV shows fall into the TV Shows header on the Zune with a separate folder/thumbnail for the different shows. The organization of videos on the Zune is perfect, the organization of the videos in the Zune software is non-existent. I could deal with the stupid policy of having to have all my videos in my collection, if I had the abilty to organized them in some form or fashion without have 146 thumbnails on one screen. It's really just a stupid way of doing things.
Who or what did what to who? That's right, he did.