Had the same problem myself - now on X1D (installing X2 in a few days - will post back if problem solved)
BUT Right now theres a big ambiguity that needs clearing up before any code fix - specifically what the automation belongs to -
Track, Layer or clip. An ideal might be that Track Automation, Layer Automation and Clip Automation each provide separate options (copy, paste assign envelope etc) and are accessible as separate entities. Currently only the clip automation is this clear cut and copying it generally works as expected. Skylight implies that copying a track that the automation belongs to the track - but the experiences above demonstrate that this isnt the case.
One solution is to put all automation in a separate stereo bus and output the track(s) to that bus - That way clips tracks and layers can then explicitly be 'attached to' the automation set - the down side is that this doesn't help with a template style automation (i.e copy, paste and modify for an individual track)