As of update 1.5.3, I can no longer assign my Fanatec sequential shifter to gear up/down in the sim. The controller is recognized fine by windows and steam, and I can see the inputs being detected in windows usb game controller settings. But I can't assign the fanatec sequential/h-shifter to any gears. I have tried creating the custom profile as suggested in another thread for a similar but not same issue, no dice. I play with a round wheel, seq shifter, and a home made button box. This bug (if it is a bug, and I suspect it might be due to the amount of posts relating to seq shifters) is effectively stopping me from playing.
There was a new Fanatec driver and firmware that just came out. If you updated to it, you'll need to go back into the Fanatec control panel and put a check in the "map to sequential" option on the shifter. The update removes that check if you had it on. I just went into the release and I'm able to assign all controls to my Fanatec shifter, so not a bug on the software end. Maybe try verifying your Steam files to be sure everything updated correctly.
Please try creating a control preset with "custom" wheelmake. That should do it. Then bind your shifter to the correct buttons. If you're using different brands.
