How can I prevent Windows 10 from corrupting the ext4 superblock every time?

I have done some research and it seems that since ext2fsprogs 1.43 (Ubuntu 16.10), the 64bit and the metadata_csum features are enabled when a new ext4 filesystem is created. I did a fresh install of Ubuntu 16.10, but before installing, I started into the USB live session and removed the 64bit and metadata_csum features for ext4 from /etc/mke2fs.conf. After this I ran the installer out of the this live session and now I can start Windows 10 without corrupting my ext4 partitions (you have to reformat your ext4 partitions during the installation of Ubuntu 16.10).

The problem is related to ext2fsd which obviously does not support the 64bit feature and/or metadata_csum feature. It is sufficient to have ext2fsd installed to corrupt your ext4 partitions. No need for them to be mounted in Windows.

You can check if these features are enabled with the following command:

sudo tune2fs -l /dev/[sdXX]

where [sdXX] stands for the ext4-partition in question.

I have the same issue and for me it seems to be the Windows 10 ext2fsd file system driver. Maybe for you too? When I uninstall ext2fsd (version 0.68) I can start Windows 10 as often as I want and the ext4 partitions stay clean. With ext2fsd installed all ext4 partitions get corrupted no matter if they are mounted or not.

I have a solution that works for me (diskpart is my friend)

1) identify the linux partition in the cmd administrative windows :

diskpart
list volume

you can see your linux partition

  N° volume   Ltr  Nom          Fs     Type        Taille   Statut     Info
  ----------  ---  -----------  -----  ----------  -------  ---------  --------
  Volume 0     D   BIOS_RVY     NTFS   Partition     10 G   Sain
  Volume 1     E   System       NTFS   Partition    100 M   Sain       Système
  Volume 2     C   OS_Install   NTFS   Partition    131 G   Sain       Démarrag
  Volume 3     L                       Partition     18 G   Sain     

DISKPART>

In my case : Volume 3

2) create a diskpart script with notepad create the file volume3offline.txt

select volume 3
offline volume
exit

3) create a bat file with notepad create the file govolume3offline.bat in the same directory

cd \users\f35\documents
diskpart /s volume3offline.txt

4) create a scheduled task Open the windows tash scheduler Program a task that launch govolume3offline.bat at boot time

5) check if all is ok after a reboot in windows

diskpart
list volume

your linux volume should be offline

Reboot in linux

If no errors => it's good
if you have errors, 
    correct them
    reboot in windows
    reboot in linux 
       If no errors => it's good
       if you have errors, goto 1)