Daniel (from Optec) here.
I think I can shed some light on this behavior seeing as I wrote the driver. The Pyxis Commander driver allows multiple clients to connect to the rotator at the same time. However several setup functions for Pyxis 2 and 3 instances require complete control of the rotator. Thus when the setup window for the Pyxis instance is open connected clients can not send commands and, as per the definition of Connected, the Connected state is set to false. Once the setup is complete the connected state is returned to true (assuming the rotator can still connect).
I had tested this behavior with several client programs, including SGP, without any issues. Given that there is now an issue I may change the behavior to pretend that the rotator is still connected while the setup is running.
Homing the rotator does not require the setup dialog. Both SGP and Pyxis Commander can connect to the same rotator at the same time. Pyxis Commander also offers a home feature under the device menu and this one will not disconnect the rotator.