Hello @skotterz!
Regarding the first issue, the Kilowhat message, sometimes the app might lose connection with the controller, in these cases, you can reload Kilowhat and it should be solved.
Anyway we’ll check if there is something else going on with your particular case.
Make sure to save your configurations regularly so you don’t loose work 
Regarding the second issue, I think your configuration upgrading process did not go so smooth.
I am checking out your last configuration and I see some trouble on banks 3 and 4, regarding the feedback on the encoders.
This issue might have happened because of skipping STEP 3 on the upgrading process described in the forum post of the firmware release
We will open a support ticket to help you we’ll continue this via email.