I have run Dualboot Ubuntu with Windows for a long time and this started to happen with me since I installed any 17.04 xBuntu variation.
Every time I boot into Windows, the next time I try to boot into x/l/gnome/ubuntu, I got initramfs and only succeed if executed:
e2fsck -v -f -y -C 0 /dev/sdaX (ubuntu 17.04 installation partition)
The strange is that I have others linux installation, like Ubuntu 14.04 and Fedora 25, in other partitions and it only occurs on the 17.04 installation.
I am using EFI partition which shared boot efi partition for all installation. It is very odd to me this and I don't know anymore what to do.
If you've got a Windows driver (like ext2fs) installed that allows you to mount/read/write to Ubuntu EXT4 partitions, then that's what is probably corrupting your Ubuntu installation. Uninstall this driver.
If you're looking to share files between Windows and Ubuntu, the best way is to create a new NTFS partition on your hard disk. Both Windows and Ubuntu can mount/read/write to this without causing problems.