And you are using the standard Logitech driver I assume? Stock G1000 or with the Working Title NXi mod?
It may be that they have changed the coding in the Asobo Pilatus G1000 so it triggers a different simevent* when you alter the ALT selector and that this new event is not recognised by the Logitech driver. It is is not uncommon for the Logitech driver to give patchy performance, particularly with 3rd party aircraft but also with some of the Asobo.
Also the WT G1000 has some custom events associated with it I believe that the Logitech driver may not recognise.
I’m not sure what changes may have been made, but someone using a specialist driver software like SPAD.next should be able to see what the events are
*this is the code that gets triggered when you click on something in the virtual cockpit or when the SIM receives input from an external controller/device