This is a problem I've experienced since Live4, but it keeps coming up.
I'll create several unlinked envelopes for a clip, mostly Clip Volume, Mixer Volume, Transpose, or Pan, and save the clip. I can immediately drag it back over from the browser and its not saved. Or I can restart Live and its not saved. I can save over and over and its not saved. This only happens with certain clips.
So about half of my clips will never save automation, and half will save automation.