I am not sure about the transparent windows - this looks like some kind of graphics driver glitch. Is it possible that you updated your GPU drivers and put your PC to sleep/turned off monitor without restarting the system? If that's the case, restarting the PC might resolve this issue.
The issue with two CMD windows appearing at system startup - this is acknowledged by our developers and started appearing after one of Windows 11 updates. Currently the only workaround is to uninstall Chaos License Server version 6 and install the older 5.5.5 version ("show all versions" here -
https://download.chaos.com/?platform=47&product=48).
To get the proper solution, we will need to either wait for our developers to fix this on our side, or for Microsoft to release a new update, but unfortunately I do not have any specific dates right now.