IIRC, when the company was formed, everyone got an equal split. They may have issued more shares when some other key people joined. But, when someone quit or was fired, they had to forfeit all shares (got paid out based on the companies revenue over the last year).

Eventually a bunch of people left and I think only two founders remained (Carmack and Carmack).

Since the stakes were reabsorbed, it makes sense why he ended up with 41%.