@Tensim The altitude hold click spot you refer to has been implemented in the Arrow since its original release in 2021, and therefore, we can confidently say that its implementation has not affected the autopilot behaviour in any way. The hidden vertical speed click spot was added in a post-release update based on feedback we received from the community and uses a similar logic to the altitude hold click spot. These clickspots use very basic logic and simply trigger the default MSFS autopilot modes when clicked, so any issues experienced with these features are likely related to controller conflicts with one of the default MSFS autopilot modes being triggered by external hardware.
One thing that has changed significantly since the Arrow's original release is the updates to the GPS units. Each of the GPS units that can be selected in the Arrow has received significant updates by their respective developers since the Arrow's original release, and in some cases, this has resulted in effectively entirely new GPS units with enhanced simulation. Each of these GPS units does attempt to overrule the Arrow autopilot code with their own custom autopilot code which can cause autopilot quirks depending on which GPS is selected.
If you would like to experience the Arrow with our autopilot code, please select the NO GPS option on the EFB, otherwise, the autopilot will be controlled by a mixture of our code and the selected GPSs code.
As Derek has said above, if you are having any issues please open a support ticket with Just Flight support we will be able to assist with troubleshooting this further: https://www.justflight.com/support
Mark - Just Flight