Have you tried turning indexing off for both OS to see if that helps? I had some strangeness happening between Linux Mint 16 and Windows 7 on a system where there was 2 hard drives installed. The first hard drive was partitioned in half with 1 half for Windows 7 and the other half for Linux Mint 16. The second hard drive was where data was stored so that no matter what OS I chose from the grub boot option, my data was there and not isolated on that other OS. I had similar consistency checks popping up with Windows 7, and I thought that maybe the HDD was failing.
I ran Crystal Disk Info to check out the health of both hard drives and they were healthy. I did some research and saw info related to Windows Indexing causing problems with dual-boot Linux/Windows systems and the cure was to disable Indexing.
I disabled Indexing and the problem was resolved.
Maybe your seeing a similar issue and disabling Indexing will cure it as well. Its worth a try
It seemed like this issue was more frequent when data was added or removed from the second hard drive, but if data remained the same there was no problems. Linux was happy with the 2nd hard drives data no matter if files were added/removed, or altered. But Windows 7 didnt like changes that occured by Linux to the second hard drive and so Windows 7 complained about consistency checks.
