I believe this to be a bug with Avogadro: initially (soon after the first installation) the main window background is fully transparent (i.e. the other windows and the desktop background are fully visible through it). After setting any color for background, it turns opaque and this setting is preserved after exiting Avogadro. However, the blue halo for selected atoms still makes them transparent (i.e. the content of underlying windows can be viewed through the selected atoms). This latter effect is persistent after exiting and re-entering.
The same problems were also detected on a different laptop, with a different NVidia GPU.
Avogadro version: 1.94.0
Operating system and version:
Windows 10 (64-bit):
Edition: Windows 10 Home - Version: 20H2
Installed on:14/03/202 - OS Build: 19042.1052
Windows Feature Experience Pack 120.2212.2020.0
Graphics: Intel(R) HD Graphics 630/NVIDIA GeForce GTX 1080
NVidia Driver: 466.77
Opaque white or black default window background.
Opaque selection halos.
Transparent default window background, turning to opaque only after bg color change.
Transparent selection halos.
Start Avogadro after a fresh install → for transparent bg
Select Atoms (always) → for transparent selection halos