Hello Rick, nice to see the Developer himself here.
(seen you in a few threads before and do find it nice on how there are plans to use a different algorithm(think it was that) to create better shapes), I stumbled upon it today and then wanted to post about it, unfortunately I entered my password wrong the first time, wasn't sure if it was this or that since I didn't use the site that many times so far(sorry, lacking time), and after entering it again wrong I had to wait for the 15 minute cooldown(guess Paint.net got attacked quite a lot in the past? two login attempts do seem a bit low, but gives me another reason to keep me logged in :P, I'm aware on how this can be bad but this is my personal PC so it's a place where I can more or less use it).
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With that out of the way, to the main post:
I've messed around with this and found a way to have it happen, when moving parts around, the old part(as in the original selection) will have the Color Values of Color 2 minus the transparency being set to 0, this is kind of an issue(even if I know that this function is there for certain things, been years but I remember Win. XP Paint doing "overlaying" via the second color.), wonder if a option can be added to not have this happen?
Thanks for the help.
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I do have a little offtopic thing regarding the circle tool, if a circle gets drawn filled, it's almost always "pixel perfect" meaning all "4 sections" are the same, however if I only draw the outline I often get something that I can't fully work with(unless it has antialiasing and is upscaled, but for nearest neighbor it doesn't really work out) think if line thickness gets set it's Radius is also bigger than the filled one, making me use workarounds to get the "proper" outline I want.
I'm guessing there might be reasons for certain things to be that way while others are more "unplanned"?
Edit:
Guess the effect you're describing(sorry I only got around reading this after posting the current situation) is what I'm having, or well, at least similar, although for me it's the second color(which with a default setup, would be black through).
Another offtopic thing but I remember reading that Paint.net doesn't save the color of transparent pixels, but it looks like it does? Might have been an outdated page.