HoMM3 HD is a mod (add-on) for the game Heroes of Might and Magic 3.

The alliance settings don't work very well. When generating, you select all the checkboxes, but when the game starts, the alliances always work, so you have to do a lot of generations.

I noticed this too. I clicked something extra, and the alliances got messed up, although the player checkboxes in the game seem to be displayed correctly. It helps if you set up the alliances last and then click start immediately after.