I thought I should add to this thread as I have also been having the same issue using a WD Mypassport Ultra. The drive was spinning whenever I checked on it and sometimes hours after it should be.
I followed the suggestion to disable desktop autorun but that didn’t seem to help. I then updated m2p and installed LMS 7.9.3 as I think I was previously running an early version. Finally, I disabled the auto start Squeezebox Server option on m2p and rebooted the Pi. Now I don’t know which, if any, of these things solved the issue but the hard drive now spins down and enters sleep mode. No vibration from drive and the light is a slow flash as it is supposed to be.
It’s only been a couple of days but so far so good!