Thanks for the responses. After some experimentation today I made some discoveries.
So I was able to get it to work properly now by engaging Passthrough Mode in the driver as long as you ONLY use the MiniDriver shortcuts for Netflix, Hulu, Etc...
The problem remains for all channels/services that there is not a Mini Driver for.
Also, even if you go to "working" service like Netflix WITHOUT using the MiniDriver shortcut by selecting "Watch>Roku Channels>Netflix" and then hit Neeo Home button you get a "Roku" device icon instead of the service you were watching and still have to go though the whole Watch sequence again to get to the transport controls.
That being said, I'm happy to have it mostly working now since there are MiniDrivers for the most common channels.
For the record, I'm on 3.13 with up to date drivers, but the issue existed on previous versions as well.
Ryan, if you need anymore info from me that would be useful to you just let me know. Thanks.