Plugging in iPod deletes my mac's Documents

I have a 5th generation iPod classic and a 2006 black macbook running Leopard. I am in college and thus don't live at home, but my iPod's library is synced to the iTunes library of my home computer, which is a PC. I forgot my charger when I last came back here and so I've been using my computer and my iPod's USB cable to charge my iPod (I have done this randomly in the past when needed without issue - this is not the first time).
My problem is that when I plug my iPod into my mac, it deletes random sets of files. For example, the first time I did it, I came back and all of my iTunes was completely refreshed; all of my playlists, music, etc. did not show up, although I did get all of my music back (it was just in the music file). The strange part was that iTunes acted as if this was my first time using it and asked me to click those agreements as a first time user, etc. It didn't occur to me that the iPod had probably done this because I had charged it off this in the past without a problem, however I now think that it did. I just tried to charge my ipod using my macbook again and it moved my dock around (I believe to the original position) and deleted all my files in the "standard" (Documents, Photos, etc.) folders. I have searched for items that were lost in spotlight and they are not showing up. I have no idea what to do, and frankly, I'm frustrated that this is happening in the first place.
Can anyone help! Thanks in advance!

How much free space on the MB's hard drive?
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