[CTRL] + [S] ??? Why did you do that? You only do that, if you want to save the single layer you are on with its alpha for some very conscious reasons.
If you want to save a png to share it here or convert it to jpeg for sharing, USE [Shift]+[S] always!
Oh, I so need a complete interface with precise information eventually, because one can never take for granted that people know all this stuff already.
Anyhow... I'm fairly confident now that there is no bug, but that you shouldn't race too fast, Pai, hehe, there's plenty of time and I hope jim will jump in to help you understand. Borhani is super sweet and very supportive, but it's challenging for him to communicate in English. Jim! JIIIIMMMM! jimmy! J I M !!! (scream)
It'll be fun!