I haven't properly used Windows in a long time, but I have a feeling the disk checking might be caused by fast startup. Basically Windows hibernates instead of fully shutting down, and the disk should never be touched while hibernated. But if you have the NTFS partition mounted in Linux, then it touches the disk anyway.
Is fast startup enabled in Windows? If so, try disabling it. It also isn't needed on SSDs and does more harm than good.