Make sure you have the newest version of dsfix. I got the one from the steam forums and it was out of date, but getting the latest one fixed it. I got the same messages and it really annoyed me for a few days!
I had this exact problem when my Dark Souls itch flared up recently, turned out my DSFix was out of date. Perhaps you have some files lingering in the Dark Souls folder from when you tried getting DSFix set up?
I had this exact problem too. It's worth looking into. The latest DSFix works though!