The Rockbox bootloader is removed by the Apple update process, since the Firmware Partition is completely rewritten.
Interestingly enough, iPods are flashable, it's just that we never do it. On the other hand Apple does, so it's entirely possible that their flash went wrong during your update, as one of the possibilities. Either way, no Rockbox software should be on your iPod in the firmware partition (the rockbox.ipod file and .rockbox folder should still be on the disk, but nothing should try to access them during the boot process).