So I installed R3E for the first time a couple of days ago and couldn't get braking input recognised in settings. I searched this forum for similar issues and found one thread about the same issue, although the solution I found there was about updating pedal firmware/software. I'm already running the latest versions so that's not the solution in my case. I've tried different braking deadzones and changing calibration settings in Fanatec software, but this doesn't seem to be helping either. I haven't had this issue in other racing sims. Whereas this is more of a speculation, my issue could be connected to something mentioned in the same thread: "It looks like a button and/or pedal has a constant contact and once you click on the reassign button it detects the pedal/button that generates the first input" - I've had two different kind of issues in two other sims that make me think this could be relevant. In one, I would unexpectedly start getting constant application of "left button" for menu selections, in the other my camera view would get pulled all the way to the left. The latter issue latter disappeared, however I can't recall any specific change that I've made to solve it. I run the Thrustmaster T300RS wheelbase and TrackIR 4 in addition to the pedals PC specs: i5 7600K overclocked to 4.8 GHz, GTX 1070, 16 GB RAM overclocked to 2666MHz, Windows 10 64-bit
Your best bet would be to go into windows control panel and select your various controllers. You will be able to see there if any of them are registered as constantly (or intermittently) on. Other than that you should be able to bind your brake by pressing it in control assignments in game. This sounds like a hardware issue rather than a game issue...
I'm not able to do this because there is no controller section in control panel other than the control panel app that lets you calibrate wheel and pedal settings through Thrustmaster and Fanatec settings respectively, and as I mentioned pedal input gets registered there normally. This actually worked just now, which is weird because when I first started having the issue I could not bind the brake control - it wouldn't get registered so the sim kept waiting for input for binding. Thank you, I hope this has successfully resolved the issue.