on some of the CDLC's i have the chord fingering / positioning is strange / unusual to me. Not  being able to play at the moment to check but... would playing the same chord in a fingering i  know work 

What is the question? Which CDLC? What fingering do you have issue with?

He's saying that the fingering on the fretboard while he's playing will occassionaly show up on certain songs, and some it wont.  But also that, he's noticing the actual chord fingering he's seeing on certain particular songs is different from how he typically would play it.  So he's wondering if he can play the chord in a way that's familiar to him, rather than the odd ball chord shape.  Did I get that right op?

As long as you play all the right notes in the chord, Rocksmith doesn't give a hoot what fingering you use!