Itunes overlapping content on multiple computers?

Basically I just got a new laptop. I copied over my entire music folder over to the new laptop, and tried to double check it would sync properly with my iphone4s. The problem is I notice that it doesn't sync all the music, only about 200+ of them with no visible pattern as to which ones are synced. I decided maybe there was something wrong so I took the phone and resync it with my old laptop, but the same problem occured there. Most of my music is not purchased from itunes store. I don't know how to fix this and searching around on google wasn't helpful... I have the latest iOS on my phone and the latest itunes. My old laptop is win7, and my new one is win8.1.