When software loaded in Kontakt 8 the s88 Mk2 keyboard does not interact with the software?
If you mean for browsing products and presets the MK2 doesn't support that with Kontakt directly. You need to load Komplete Kontrol then load Kontakt inside that. For direct Kontakt integration you need a MK3 keyboard.
If you mean something else isn't working as you expect let us know.