This problem was a headache for me also.
I have fixed it.
My solution is, step by step:
1- back up of presets, cabs, layouts of the firmware I am going to leave (I skip system backup, not necessary for this)
2- reset system parameters (FM3 unit>Setup>Utilities>Reset page>ResetSystemParameters)
3-install new firmware
4-after rebooting the unit, reset system parameters again
5-set manually again all system parameters (only import layouts)
This solution has worked for me perfectly for 3.03 beta1, 4.00 beta 1 and 4.00 beta 2. In fact, I will always install firmware in this way.
It's important to remark step 5: if you import system parameters from a backup, the problems can be imported too. So it's important to set manually the system configuration.
Finally: to do step 5 it's important to have a list of what parameters must be changed. Not necessary to have a list of all parameters of the unit (a lot). It's only necessary to have the list of what parameters must be changed from default values (when reset system parameters all parameters are set to default).
I did the list like this:
First, I took a picture of every page of the setup menu in the unit (scrolling down also for the largest pages). These pictures show the parameters you want to have in the system. So, these pictures are taken before resetting the system parameters.
Once I had the pictures, I reset the system parameters, and I navigated again through the menus of the unit and compare them with the pictures. The parameters that are not coincident is the parameters you should be aware to change from default values. You can write that parameters in a list, and/or highlight in the pictures.
Once this list is done, you just have to focus on that list parameters when doing step 5 every time you reset the system.
Example: In I/O menu, Audio page, I only change the USB 3,4 Playback destination to Output 2. This is the picture I have, with a red rectangle around the parameter:
View attachment 83929
I wonder if FAS should recommend reset system parameters before/after installing in the release notes.
It may also be interesting to have a checkbox in fractal-bot when installing firmware, asking for installing the firmware with a clean installation. resetting everything.