I've been having the same issue in Pro Tools on Windows 10. But I came up with a workaround, it amounts to way more setup and maintenance than you should have to do, but it works – when I follow these steps, my Arturia plugins (currently using Mellotron V and Mini V3) always come up with the correct patch/settings when I open the Pro Tools session:
1) In each plugin, save the current patch/settings as a Preset in the Library, if it isn't already saved there. Do this for each plugin instance that has a different patch.
2) In each plugin, create a new PLAYLIST.
3) Drag the saved preset(s) into the playlist, in the order you want (or drag to rearrange afterwards).
4) Insert a program change automation message at the beginning of each Arturia track, corresponding to the preset's position (starting with 0) in the PLAYLIST.
5) Open all Arturia plugin windows, by Shift-clicking each plugin so it stays open.
6) Always leave all Arturia plugin windows open, simultaneously, when you close the Pro Tools session.
To Arturia: maybe the above workflow will give you an idea of how to fix this issue? It's ridiculous that your plugins can't recall their settings properly unless the settings are saved in the Library, included in a Playlist, and the plugin window is open when you open your Pro Tools session!