This usually happens if you have Fast Startup enabled in Windows (as it is by default in Windows 8 and 10).
When shutting down with Fast Startup enabled, Windows does not really perform the complete shut-down procedure. Instead, it ends the user session, minimizes its memory footprint and essentially hibernates. What it does not do, is the equivalent of properly unmounting any local filesystems. If Windows is the only OS on the system, that's not a problem; but if you're dual-booting, it causes the exact problem you seem to be having.
Disabling Fast Startup should elimenate the requirement to routinely run