You don't mention what you're doing in Enahnce, but if it is Denoise then of course Denoise does both luminance and colour denoising. So with starting colours being different (V6 vs V2) then you would expect it to be different.
By how much though? And can you (easily?) modify the DNG after the switch to V2 to give you want you need? Can you post before/after examples? (V2 raw vs V2 DNG)
I would imagine this would be different from image to image as well (depending say on saturation, and noise levels).