If Windows is running
CHKDSK at every boot then you have a problem.
CHKNTFS to exclude the drives from checks at boot is not a good idea at all, that's just ignoring the problem.
If you are ensuring you always shutdown properly, and it appears to do so, then something is causing the dirty bit to be flagged before power off.
This can be caused by many things (hardware or software), and it's impossible to pinpoint based on what we know. But it's most likely a hardware issue (based on too many years of experience). If you have warranty, save your data and get them to fix it, should be EASY for them if it's happening every time (and they should have all the spare parts available).
If you want to try and diagnose it yourself, then please go try a few things and come back with specific questions.
Hint: try Windows power adjustments, and HDD manufacturer diagnostics to start)