I’ve installed Avogadro 1.2.0n on two Windows x64 boxes.
On one PC Export → PNG gives a transparent background as expected (PNG has alpha layer).
On the other PC, the same CML file exports a PNG with the same coloured background as the Avogadro view (PNG has no alpha layer).
The transparent PNG is from “Intel® HD Graphics 630” (as provided by the i5-7500 CPU) and the standard Windows Update drivers.
The coloured background is from a nVidia GTX 980 video card and the latest 451.67 drivers.
Is there a setting somewhere in Avogadro or nVidia control panel that might affect this?
The test image in question was just File → Import → Fetch by chemical name → Ammonia.