the new pt-hub -controller pakage installed by the new PolarisOS gets broken if you run
something about the newest bleeding edge kernels causes the pi-top's hup to randomly darken and brightn the LCD screen. it also cause random shutdown signals to be sent to the pi causing the shutdown of the systems without any action taken to do so. also the hub won't accept attempts to lighten the LCD sceen from the keyboard or through software without many repeat attempts.
On my pi-top installing the latest kernel (uname -r shows 4.9.13-v7) does also show random brightness changes and random shutdowns with pi-topOS.
The way pt-hub-controller works is that it reads brightness and shutdown info from the hub using the spi interface. Then it writes back the same or modified values (modified if the user has requested a change). The problem with this approach is that if the reading fails, wrong values such as wrong brightness settings or even shutdown requests will be written. Unfortunately, the spi protocol has no error recognition or recovery whatsoever. Therefore, things will go wrong.
I have seen that you are wrestling with this problem since a while. I am sure you have already or will soon report this to pi-top support.
thank you for your input rene. I will report this to pi-top support soon. if you don;t mind, I will copy and past your response , since it is less cluttered than my own...