From your description. it sounds as if your irises are infected with iris borers. These attack the base of the stems and tubers, tunnelling into the tubers which are then often attacked by bacteria and become mushy. In spite of removing the damaged tubers and surrounding soil, it is difficult to eradicate the problem. I suggest you repeat the soil removal but don't replant in the same part of your garden. The adults lay eggs that overwinter and these will hatch in spring and tunnel into new growth. Be sure to buy healthy, pest and disease-free tubers from a reputable source.