Messed up colors in fullscreen sounds like a driver issue. As for the windowed problem, is whatever shortcut you are using pointing to the .conf file you are editing? The one you posted (the combined .confs for MM3?) still has the game launch fullscreen. Change fullscreen=true to fullscreen=false and save the file. If the game still launches fullscreen then you are editing the wrong .conf or using the wrong shortcut.

What's your hardware, and monitor if separate, anyway?

Specs: I5 2500k 3,3 ghz, 8 gb RAM, Nvidia 8800 gt, Win 7 ultimate 64. Monitor: Hanns·G HG-281DPB.

I renamed all the other conf files to .confbk just to be sure it wasn't accessing one of those by mistake. Same thing. Small window. Even with fullscreen=true, it launches in a tiny window.

Something is off there. With fullscreen=true it would launch fullscreen, tiny & in the center if unscaled, but without the rest of the desktop being visible. What's the Target and Start in lines of the shortcut properites?

Target: "C:\GOG.com\Might & Magic VI Limited Edition\DOSBOX\dosbox.exe" "C:\GOG.com\Might & Magic VI Limited Edition\Might and Magic 3 - Isles of Terra\Mm3.com"

Start: "C:\GOG.com\Might & Magic VI Limited Edition\DOSBOX"

Just tried running MM4-5 and I am having the same issue. So it's not just related to MM3.

That's likely the problem there. Change the target to: So, remove the mm3.com part and use the actual path to the .conf file you are editing.

I'll try it, but I was having the same issue before I made the shortcut.

Like this?

Target: "C:\GOG.com\Might & Magic VI Limited Edition\DOSBOX\dosbox.exe" -conf "C:\GOG.com\Might & Magic VI Limited Edition\Might and Magic 3 - Isles of Terra\dosboxxmm3.conf"

That doesn't launch the game. Then I have to manually mount the path, which is a pain with Windows directory names.

Yes. Does that file have the [autoexec] section in it? The mount C line you posted above would be wrong at any rate. Simpler to use the full path: You can also comment out the exit line while testing by placing a # in front of it.

Okay, got the shortcut figured out, I think.

Target: "C:\GOG.com\Might & Magic VI Limited Edition\DOSBOX\dosbox.exe" -CONF "C:\GOG.com\Might & Magic VI Limited Edition\Might and Magic 3 - Isles of Terra\DOSBOXMM3.CONF "C:\GOG.com\Might & Magic VI Limited Edition\Might and Magic 3 - Isles of Terra"C:\GOG.com\Might and magic - Isles of Terror\mm3.com

This launches the game, but it's still in a small window. I tried manually mounting the directory and launching the game, as well. Same thing.

No, that's not what you want. Just include the proper commands in the .conf file. If it's not launching the game then you have typos either in the shortcut or in the .conf file itself. In which case you should fix them.

I'm not sure I understand what you mean. I have edited the conf file, but it doesn't help. If the shortcut is the issue, I have tried manually doing the following:

1: Mount c (mm3 path)
2: C:
3: mm3.com

This launches the game but still in a window.

The shortcut should be loading the .conf file that you edited. DOSBOXMM3.CONF in this case, note the closing quote. In DOSBOXMM3.CONF you should list the commands to mount & start the game. Which means if the shortcut is configured to use DOSBOXMM3.CONF and DOSBOXMM3.CONF is configured to launch the game then the game should start automatically. If it isn't you have an error somewhere which needs to be fixed.
If you are just launching the executable or COM file in this case then it's not using DOSBOXMM3.CONF settings and you get your tiny window.

Cheers.

Glad you got it working! Also, Gydion is correct that the GPU scaling only affects fullscreen, that was my mistake.

Enjoy the game!