I have exactly the same question.
I think all other image editing programs do exactly what it is meant to do - as in it physically 'saves' right away when you hit the enter button, or if we click on the 'save' button. I don't expect a software to make me jump through a hoop after I specifically had hit the 'save' button, and then the software pops-up another window that then makes the user need to click on 'ok'. And if they don't click on that 'ok' (and not be aware of it), then their work becomes lost when they inadvertently close that window - which should ideally have been saved upon the users specific command, but the system didn't save because of the need to further click on 'ok', which is counter-intuitive.
It's ok if users get a choice though, as in having an option that prompts a user to save - as in 'are you sure?'. But otherwise, the default setting should be the usual one - where the user hits 'save' (or pushes the enter key) - and then software just simply needs to do what it is meant to do - and save.
The OP is not referring to 'save automatically' or automatic timed-saves. The OP is referring to users getting taken by surprise all the time, because they assumed that the software did what is expected - that is, it should save unconditionally when the user clicks on 'save' (or when they hit the enter key). I'm pretty sure that many users will have been caught off guard by this particular behaviour with paint.net, where the software isn't doing what it is meant to do - as in just simply 'save' when the user pushes the 'save' button. And the user later comes back to their computer on some other day, just to find there is no 'image' file there in the directory, because the system did not save the file.
