Saving on the MPC 2XL

I have had trouble saving on the MPC. I have been saving a program(with replacing same sounds), and saving all sequences. But when I load up the program and all sequences out of its folder, some of the pads have switched. When you guys save, what are you doing that i'm not. I'm a newb, so could you walk me through this.

ALL is all mixer settings and sequences.
APS is all programs and sounds.
PGM is a single program.

I usually save ALL and APS.
When I turn on and load my
MPC2kxl again it's all there
just as it was at my last save.