Mine does the same exact thing but I haven't done anything to it at all the software is completely stock, I even factory restored it. I have been told that if you take the phone apart that it knows and considers it custom.
The only thing I can think of is that I got water in it and had to tare it all down to dry it all out and it broke my speaker so I got a new speaker and replaced it so it works fine now. But can it really tell that its been open to expose the circuit board??