I tried setting a pad note value on my Keylab 88 mkii and it worked correctly. I think the interface is a little clumsy, though.
In Midi Control Center you have to (a) select your keyboard (b) select your template i.e. "User 10", (c) select the pad to change, (d) change the note as desired i.e. C3, (e) save the template, (f) Sync the template to your keyboard ("Sync to").
Then on the keyboard select "User" mode and your saved controller mapping i.e. "User 10". I then find that when I press the pad, the keyboard shows the note I selected for it, and plays that correct note.
Sorry if this is all stuff you know--I'm just figuring it out myself actually.