The only way I can see this happening is if you have different ME routing selected on each scene.
For example: If you had Kick, Snare, Tom1, Tom2, Tom3 all going to ME 1-5 respectively on scene 1 and then you set up your groups and layouts etc.
Then if on scene 2 you have Kick going to ME w and Snare to channel 1, it will completely mess with the ME1 and it will likely have to resort to just assigning the buttons in order 1-40.
If I were you I would double check that your scenes all have the ME “outputs” or channels tied to the same inputs.
I am not 100% sure on this, but the I/O assignment shows all the input channels in order. So if on a second scene your input channels are all out of order on the mixer that might be causing the issue also. Either way it’s really the same problem.
I would think that it would follow inputs, but maybe there is a setting for that.
I would go to scene 1 and check your ME channel assignments and make note of them 1-40. Then go to Scene 2 and do the same thing and note any differences and correct them to match Scene 1. Then, go back to Scene 1, setup your ME1s and then go to Scene2 and see if it stays the same.
Good luck