I have some experience with the Lisa/S and the usbrf. I've had the same problem you have now. I was facing several problems. I was attempting to run paparazzi on a virtual machine, and the VM I was using was having trouble letting my usb ports communicate through, and I thought that was the source of my problem. When I eventually reformated and went with a native Linux install, I was still facing the same problem, and this time, I thought it was because of the Black Magic Probe I was using, that was getting ACM0 allocated to it, while the usbrf fell over to ACM1. When I fixed that, my problem remained. I had already confirmed with a "dmesg | tail" that my usbrf was properly detected and my udev rules were properly setup.
What ultimately fixed the problem was the binding procedure. When you plug in the usbrf and you want to bind it to your remote, you have to make sure that you're pressing the bind button on it. Ditto when you power on the Lisa/S. Don't try to bind them both at once, look at the flashing lights to make sure the binding occurs. If everything is properly communicating and the signal still doesn't get through the GCS, I still have a few more ideas, just let me know.