In a medium skillet over medium heat, combine the ground beef, garlic, onion, and bay leaves. Cook for about 10 minutes, breaking the beef up with the back of a spoon, until browned. Drain, stir in salt and pepper, set aside.
In a medium bowl, stir together the tomato paste, chili powder, flour, cumin, and thyme.
Put the pinto and kidney beans in a stock pot.
Add the ground beef mixture and the tomato mixture and stir until combined.
Slowly add the water until the desired thickness is reached. (Less water for thicker, more water for thinner.)
Turn the heat to high and bring the mixture to a boil. Reduce the heat to low and simmer the chili for 10 minutes.
Remove and discard the bay leaves before serving.