Sorry, Peter but my tests show the big problem is that ST3 forgets the locations of all loaded patches if the project is saved, closed and then reopened inside the host (Sonar and Studio One). The same thing happens if you save the loaded patches as a Multi.
Standalone behaves the same for Multis, e.g. open, load some patches, save the scene as a test multi. Close standalone. Reopen. Load test Multi. Locations not highlighted when any track/patch is clicked on.
I'm eagerly awaiting Support's response to my ticket. This is really bad for me as I use ST3 a lot. If a fix is going to be a while then I need to know from them how to roll back in the meantime to 3.5.