In his mushroom growing books, Paul Stamets points out that the quality of rye can vary greatly and that some brands/batches of rye have a lot more endospores than others. Perhaps even good quality rye seeds have more endospores than brown rice flower. Perhaps when pressure cooking, the steam can't reach all parts of the seed as easily as it can with the brown rice flower, affecting sterilization efficiency.
Stamets also advises to soak the rye seeds in water for 24 hours, to trigger the endospores out of hibernation. After the soak, discard the water, rinse the rye with clean water and sterilize in a pressure cooker.