How long are you leaving between turning on your modular and tuning and playing?
if they are digital modules it should make no difference, but analog modules need sometime (anything up to 1/2 an hour & possibly more) to warm up and stabilize... if you tune before they are stabilised they will go out of tune whilst you are playing...
with marbles for all 3 X outputs to output quantized notes related to the settings on the panel you must set the X mode (button N in the manual to green) - if you have a different colour displayed on the related led, this may be the problem
https://pichenettes.github.io/mutable-instruments-documentation/modules/marbles/manual/
"some of the best base-level info to remember can be found in Jim's sigfile" @Lugia
Utility modules are the dull polish that makes the shiny modules actually shine!!!
sound sources < sound modifiers < modulation sources < utilities