I tried to test nQuant on this image:
The results were not good (see attached image). The alpha channel presents discontinuities.
If you check the resulting image in a editor tool, and display channels one by one, you can see that the R, G, B channels are fine, but not the Alpha channel.
Maybe I'm just missing a setting though, I'm, using the default settings in nQuant.exe:
private static int alphaTransparency = 10;
private static int alphaFader = 70;