Hey, will try and help here.
First I’d check that you don’t have any other PCs for the JU06 in any other tracks or patterns or step/automation controls. Or FX (there’s a note # to PC MIDI effect!) Indeed, you should also check for any PCs anywhere else that are being sent on the same MIDI channel and MIDI A/B output.
If you only want this one to be used as your default state for this project, make sure you aren’t sending any out that is instructing the Ju06 otherwise. Really easy to lose track of these things in and amongst multiple tracks and patterns and automation.
You might be saving a PC into a track or pattern that is ‘playing’ at the time that you save. Then when you reload the project, Pyramid is looking at PCs that are going to happen when you hit play, or are in active/inactive mute states and/or Sequences depending on what your project looks like when it loads.
Also I’d check the JU06 spec/manual and see if you need to send a Bank change (usually defined by MSB/LSB setting) at the same time as your PC. But maybe you figured that out already cos you got your PC right when you saved it, yes?
Let me know how you get on.