Pad Settings are saved to the actual pad and NOT with the sample!
I actually see this as a great feature becuase it means that, in practise, you don't have to set anything when you load in a new sample/kit!
EG: I have banks 1-9 set aside for multisamples. I can set up the pads in these banks so that they always play the multi's the way I want. I usually have multi's spread across two banks (nearly a 3 octave range), so I can set up those banks so that they are 'multisample ready'... So banks 1+2 are set to gate; mute-group 1; mono for a classic monosynth sound...
Banks 10-20 are 'drumkit ready'; shot play; mute group 10 (for all hat sounds); mono.
The last 12 banks can be left for loops and phrases!!
If you set up all your pads like this you wont have to adjust anything when you load up a kit or multi!!!