Really? What software did you use to extract the file?
I always used to mount system.bin as a raw image since it was the easiest way for me, and that was the file that I got out of it.
It's seems (at least in my case) system.bin is merely a container (zip container?) of files as opposed to an actual binary file. I simply right clicked it and told 7zip to extract the bin file. When 7zip was done I had a folder on my desktop with all the files that were encased in the system.bin file.