Messed with it but couldn't seem to replicate any issues. Anything more specific I should try or maybe take a screenshot of your controls window? Also are you using a pad or an arcade stick?
I changed R1 to
Rapid Speed. Set X to
Shot with My Rapid Set enabled. Hitting R1 cycles through 10-12-15-20-30 as expected and shooting with X shoots at the set expected frequency. Pause menu and all that still seems to function all as normal, but maybe I missed something?
Oh, or maybe you've mixed up some of the options? Take a look under Controller Setting here maybe that will clear it up.
https://shmups.system11.org/viewtopic.php?t=58944