Well the QC now controls EQ as it should 
The issue with going into Midi mode when quitting Cubase is as jgaryt stated “by design”.
This is explained in the Operating Manual.
The QC can function as a standalone midi controller when not being used in Cubase. In order to facilitate this, it must be in midi mode. If it’s just the knobs being lit, I believe you can change this e.g. using the editor.
I’m not saying your request is wrong, I’m sure that this behaviour could be made an option. So, perhaps in a later update…