hi there, sorry, don't understand, if you do exactly as you describe, the pad will be recorded normally.
Are you sure the track you are using is assigned as the control track? You can't use Track 9 without first assigning it as the control track, and you cannot have 2 control tracks at the same time.

The disadvantage of real time recording the control track again is that you have to repeat all the panel memory, variation, fill changes all over again, and get the ending in the right place again too.
Much easier to go into step record of the control track and put the Pad (and the Stop if required) at the relevant points, and take care of the balance in your panel memories.