@TheOtherCliff
There is actually a "problem" with SPI flash on that board, as it appears they used few different types of flash (from different manufacturers) and our current spi flash code does not allow for that type of flexibility, so .. yeah, it probably sees 0 amount of settings storage free, therefore no saving possible.
I did already move settings to mcu flash in my private branch on this board for that exact reason (the other types of f3 do not even have spi flash, so they use internal flash anyway), and have plans to use external flash (or sdcard) for logging only, together with some improvements in jedec flash code for chip type and geometry detection at runtime.