In short: I save in PNG, it works fine for me, I share and give it for free common use.
Don't blame the file format if a tool isn't meant for the job! I don't have much experience on Paint.NET, I only remember I tested it and didn't like it. What I've downloaded some of the BMP files on this forum they are often/always full color (16.7 million colors) and not paletted. This has lead me to think that RttR loads non-paletted BMP images and is hard written to understand certain color values to work a certain way. I haven't tried to use any graphics in RttR, because at this point I'm more interested in figuring out how the original game works and how I can modify it.
As for tools, I use Paint Shop Pro 7, and it retains the palette as it is. However when drawing new pixels it prefers using the first item in the palette that matches the same color. For this reason I made my own palette that has each color unique. This shouldn't matter when the images are loaded by palette color index (ie. ignoring the palette & their color values), but seeing that there have been problems with these files it looks like the actual color value is trusted more than the palette index, leading to problems with my graphics in RttR.
For the original S2 the palette index values are the thing to trust. For example I can save LBM files with whatever "incorrect" palette colors I want, but if the palette indexes are OK in the image then it displays correctly in S2. Even if we look at the game's files the texture files are saved with an incorrect palette (if compared to the palette used in-game). I actually save all my modified textures in PNG (with my palette) and then use Graphic Workshop 95 version 1.1y to convert the textures to LBM format S2 can read (and it still has the incorrect palette). Doing this is as simple as clicking a file, click a button, select LBM, and then I have both PNG & LBM in the same folder. So no problems here. Of course LBM is not the only file format used by S2, but when I start dealing with LST/IDX/DAT/BOB I'll probably output to/input from PNG.
As for my lack of testing things with RttR... partially things are like this because RttR isn't a non-German friendly project. You download a Windows installer, it is in German. This site is almost entirely in German. The domain is siedler25.org which is not friendly for international audience. Selecting English doesn't make the site English, it even breaks some things (inability to change avatar, can't start new threads...). Things like this don't make RttR an attractive project for non-Germans. So this is also why I prefer modding & figuring out the original S2 over working with RttR. But it doesn't prevent me from giving something S2-related for RttR if it is easy enough for me to do so. The new Greenland texture is made to work with S2, not with RttR, but it is kind of more useful thing for RttR. I made the other graphics mostly because I like drawing pixel graphics.
Now if we could continue with the new Roman graphics topic instead of talking about the file formats all the time.
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