I think it would help if you could please confirm the exact version you started running when the issue started occuring. You mentioned in the original post:
Are you saying that the issues started happening when moving to .157, to the most recent public release (2.4.2.158), or onto a more recent beta release?
While not complete absolution, the release notes for 2.4.2 around this version doesn't appear to offer any possibilities.... even with the Z-Wave updates.
For all you have described, I would say it does sound odd and like there is something not right somewhere. I am likely to not have read everything closely enough, but have you mentioned what driver you are using for the motion sensor? Given a variety of HE apps are not firing I am wondering if it is something to do with how the driver is raising the events within HE that is causing HE apps to respond differently to HA automations.
