I'm looking at the manual... first question is track type. On p. 228 are you using track type = Acc (accompaniment), or guitar? Even though it's a guitar lick, I would use accompaniment for this purpose.
The next settings you need to look at are described on p. 244. NTT should probably be parallel. On the next page, I would choose 'Parallel / No Transpose.'
Give these settings a try and see if your original notes are preserved.
I guess the question I should have asked at the beginning is, do you want this pad to "chord match" like a style track? I.e., do you want the arranger to transfer the guitar lick in real time based on the chords you're playing? Or do you just want to play along with the guitar lick in its original key? The latter is easier to set up. -Ted
P.S.: Yamaha has a setting in their style creator about whether a particular track is a 'phrase', chord, pad, etc., and does restrict notes recorded on "chord" tracks to certain degrees of the scale. I personally never tried a custom backing sequence with dissonant notes on a Korg, but there's nothing in their documentation suggesting these notes would be ignored or not transposed.
Edited by TedS (09/22/16 05:37 PM)