Yes there is a marked difference. The issue ones "feel" higher quality, I don't know how to describe it better. The cloth should be ripstop nylon, the camo colors should be dark and crisp. They are not as "fluffy" as the knockoffs.
Keep in mid though that some of the ones sold in surplus stores are issue (if you can find them) seconds, came from the same factor but have cosmetic flaws. I have also seen knockoffs that were extremely well made. The ones sold at places like Ranger Joes, Brigade Quartermaster etc. typically have pretty high quality copies.
I have plans on making a underquilt from a liner also, but am going to use a knockoff as I would hate to hack up a now hard to find issue one.