This achievement appears to be bugged in the Windows 10 version at the moment. From what I can guess, it seems that the game will register a cleared board for each time you press the 'New Game' button prior to actually clearing a board the normal way. So I believe you should be able to do the following to get the achievement:
1. Start a new game.
2. Press the 'New Game' button 99 times.
3. Proceed with your game, clearing at least one board normally
4. Get Achievement
I found this by accident after having my tally for the achievement skyrocket after attempting to find a game with a King at the top of the pyramid for one of the other achievements. It doesn't update the statistics screen (I only have 27 cleared boards at this point), only the tally for the achievements.
This trick works for both Pyramid and Tripeaks.
Thanks to BB rocker for discovering this only works for the Windows 10 version.