I was having similar problems with my M7 and Windows 7 devices after upgrading to 4.4.2 and Sense 6 (Team Nocturnal NuiSense). My phone wasn't recognized by HTC Sync or CDMA Workshop.
I kept uninstalling/reinstalling drivers, to no avail.
What finally worked like a magic bullet for me was to dial ##3424# and turn on DM Command Service.
I'm not sure if that will work for you, but it may be worth a shot.