@bigbugz420 Enable verbose logging in Runcommand (https://retropie.org.uk/docs/Runcommand/#configuring-runcommand) and then get the log file from /dev/shm/runcommand.log after launching a ROM and not being able to control it with the controller.
Paste the file's contents at pastebin.com and then show us the link.
You still didn't say how are you connecting the controllers - is it bluetooth or USB ?