Some thoughts about a couple of possible causes (that may not apply; there may be more info on this in the Github for the project, or it's wiki or threads; I have not checked):
I don't know how the firmware / flashing process is written for this OSF, but I've often enough run across devices (of all kinds) with firmware updates that flash the software, but not the *settings*, yet use incompatible settings data between the two FW versions. Some of them advise the user to reset everything to defaults manually, using whatever "factory reset" function there may be, but some don't.
Some may not have a settings reset function, but for those it may be possible to manually write values to all the fields to do the same job.
It would be more failsafe if they always actively reset all the settings fields (used or not) to defaults for that specific firmware at the same time, but this is not always done.
On occasion, some do a kind of reset, but they first check if a setting is already default and don't write to it if it is, yet somehow the setting is not really at that default (perhaps a single-bit difference where that bit isn't checked for some reason), so the corrupt or incorrect value persists and later causes a problem with the firmware trying to read it back and use it to do things with. Some may not check any settings but may only write to a few of the locations, attempting to preserve user-settings or "calibration" values, that end up being incompatible with the new FW.
So if there is the option to do a full reset, something that actively writes that specific firmware version's default settings data to *all* settings (including all fields regardless of what they are for), it might fix a problem caused by this particular issue.
It would force you to set every setting back up again, but if it works, it's worth the time.
Another potential issue is if there are files with your settings being used to reset the device to particular setups, *those* could have incompatible (or corrupt) values within them causing problems. Ensuring you manually change each field in the setup software to the correct new data (perhaps even changing each field that appears already correct to something else, then back to the known-correct value, before flashing the new settings) might work.