Combine rice and water in a saucepan and bring to a boil. Reduce the heat to low, cover, and simmer for 35 to 40 minutes, or until tender. Remove from the heat and let cool.

Meanwhile, rinse black beans and pinto beans in a colander or strainer. Transfer beans to a large bowl. Mix in corn and diced tomatoes with green chiles, then mix in cooled rice and pepper Jack cheese.

Divide mixture evenly among tortillas and roll up. Wrap individually in plastic wrap, place into a large freezer bag, and freeze.