Take a look in the SMP2 menu of the SINGLE EDIT mode. There is a parameter called ‘Out’. The ‘Out’ parameter found on this page functions as an ”offset” to be added to the original output selected for the entire program. So, in the case where the program is assigned to Output 2 and sounds are coming out of Output 3, the ‘Out’ parameter is probably set to +1. Change this parameter to zero and you should not have any problem assigning the program to Output 2.
As another example, let's assume that you have a program with two keygroups. Keygroup 1 is a bass drum and Keygroup 2 is a snare drum. Set the Keygroup 2 Out parameter to +1 and then assign the whole program to Output 1. The bass drum will now appear on Output 1 and the snare on 2. Change the Keygroup 2 ‘Out’ parameter to +2 and the snare will appear on Output 3! Now change the program Output to 2. The bass drum will be on Output 2 and the snare on 4, etc.