I've had this same problem for years now.
I noticed that for me Clip Automation doesn't work but Track does.
This is a hard one to reproduce since in my case at least it seems to be totally random. One run through and all is well then the next few nothing, then all is well for a few more runs.
I just use Track Automation now all the time.
I have also tried to move to a new project and no difference.
Sorry if this is no help but until there is a way to reproduce this consistently it makes it tough to trouble shoot.
Mike