Certain firmware revisions also update the gamecard controller (lotus) firmware. This can cause issues if your firmware version and lotus firmware version do not match.
At the time of writing there have been 4 firmware versions that updated the lotus firmware: 4.1.0, 9.0.0, 11.0.0 and 12.0.0. The lotus update is applied by the bootloader, meaning if you boot using the stock bootloader (note the "stock" option in hekate does not do this) your gamecard controller will be updated.
Once your lotus firmware has been upgraded, it cannot be downgraded. Additionally, you will be unable to use gamecards on any firmware lower than the version that updated your gamecard controller.