I'm not sure, but this sounds like some kind of compilation error maybe, or an error in how you're calling the ptx file from matlab. It might help if you posted your code. Basically matlab is parsing both your .cu file and your .ptx file, and it's finding that they have different numbers of input arguments.
Since both the .cu and .ptx file are plain text, you might be able to skim them and see whether they have the same number of inputs. (The ptx is not quite human-readable, but you should at least be able to find where the inputs are defined)
Edit: might also help to see exactly what command you're running to compile the ptx file.