i have a problem with controller too, but it's a little different:
i use mouse to steer and keyboard for anything else, both usb.
most of the shifts up and shifts down are missed if button control rate is set to maximum the problem is less evident, with button control rate to minimum, it's almost impossible to change gear especially if any other key is pressed, the strange thing is that with the new car, this problem is really evident while with other cars much less.
at first i tought it was a new "feature" of realism, where autoclutch was removed and throttle must be released to change gear, but this obviously not the case.
PS thanks for this new update, the new engine moment of inertia greatly improved realism of cars!!!