I know you said you updated your AClients, however, did you upgrade your DS? I think if you are running 6.9.366 on the AClients, your DS should be at 6.9 SP1, MP1. If you haven't done this, this may be the reason that you are having a problem with the "correct logged on user" not showing up in the console.
As for the remote control issue. This may also be an issue if your server version doesn't match the client version as close as possible. I am running 6.9 SP1, MP1 and the AClient 6.9.366 and DS Remote Control works fine for me.
You might also check the Event logs on the target computer just to see if there aren't any warnings or errors that could shed some light on it.