I've had this issue constantly.
Sometimes I've fixed it by unplugging and replugging the controller, sometimes it just fixes itself.
This morning it wasn't detecting my 2nd controller, and after restarting my pc, now it only detects 1 of my 6 fans at all and a warning for controller 1 pops up.
I uninstalled the software and used the TTController instead and it detects all 6 fans so it's 100% this ####Tt RGB Software that's broken, not your setup.