Maybe this INDIV/FX source setting, quoted below from the manual, is set to PROGRAM, so that it is loading up the individual output mixer assignments and levels from each newly loaded program as it loads, which maybe didn't have the individual outputs assigned and levels set when it was last saved (so it is turning them off, setting the individual output assignments to be unassigned and/or setting the individual output levels to be zero)...
Setting Up the Mixer
Hold down SHIFT and press MIXER (numeric key 7), then select “DRUM 1-4”.
The mixer display will appear.
Press SETUP [F4] to display the mixer setup screen.
Mixer setup
Stereo mix source:PROGRAM
INDIV/FX source:PROGRAM
Copy pgm mix to drum:YES
Record mix changes: NO
Master Level
0dB
FX drum
Drum:1
In the Stereo mix source: field set the Stereo Output mixer and in the Indiv/FX source: field set the Individual Output mixer. The following parameters can be selected for either one.
PROGRAM
When you select this mode, the mixer or individual output settings change to the settings of each program.
DRUM
This records the mixer or individual output settings within ALL PROGRAMS (the data extension when saved is .APS) which applies to all programs and sequences. When you select this mode, the mixer or individual output settings will not change when the program or sequence is modified and the DRUM settings will always be applied.
Copy on pgm mix to drum:
To COPY the mixer settings of the program to DRUM when the program assigned to drum is to be changed by Program Change.
If INDIV/FX source: is set to PROGRAM at the moment (which it sounds like it might be), maybe load and setup each program with the individual output assignments and levels that you want, and re-save each program like that, so that it loads up the correct individual output assignments and levels, as you want them for each separate program, as each program loads (you could have differing assignments/levels for each program with this method).
Or, set it to DRUM, and make sure that you save, and load each time when you start to use the MPC, an ALL PROGRAMS file that contains the individual output assignments and levels as you want them for all your programs (this might possibly only be useful if you have a single set of output assignments and levels, which you want to apply with exactly the same settings to all programs that you work with).
And maybe experiment with the Copy on pgm mix to drum setting, to work out what that actually does to the individual output assignments and levels when you change programs. It sounds like it might keep the mixer settings from the previous program, and apply them to the newly loaded program, but what it actually does isn't clear to me from the quoted description above.