Hmmm, I so rarely work regular drives so I'm trying to think how we would need to do it there. I think your shared folder tactic should generally work at least, so let's give that a try. (but I don't think it should be required when using the latest version).
When you did this - did you use the --drive-shared-with-me flag to get access to them? That may be needed. You probably need to copy them from user2's "shared with me" folder rather than using user1's files as the source in the copy operation.
(But I must admit I am a little confused as to why you managed to copy some files but not all).
Just so aren't making a simple mistake - tell me what method you used to activate server-side transfers. Did you use the flag method or the config method (and if so, on both remotes or just one)?
@ncw Am I forgetting something here? 