Based on Frostschutz's investigations
here it appears that the current Kobo firmware is writing to part of the FAT filesystem that it should not be. (see
this doc esp. section 3.3, for reference on FAT fs)
In Win10AU MS have decided to enforce some checking where previously they did not. If, as has been speculated, this is as protection against malware then you can expect them to also disallow drivers that try to bypass this check. I was reading just the other day that drivers from now on will have to be submitted to MS for signing.
The proper fix for this is for Kobo to update their firmware to stop messing with the reserved part of the FAT filesystem. They are apparently working on a firmware update so that's good.