I've got exactly the same problem with missed upshifts (and, I think, downshifts) using sequential shifters. I only use AC but it sounds like the issue is unique to that sim.
I had a similar problem a few years ago and solved it simply by remapping the keyboard bindings to different keys, but the issue recently came back and I've tried all sorts of keyboard bindings with no success. Like you, I also tried a plethora of different debounce settings.
I have a Fanatec Clubsport shifter and a separate sequential shifter (your old one!), and also want to use paddles when appropriate, so it seems I have to use secondary bindings and 'combine with keyboard' to keep all options available.
In CM/Assetto Corsa/Controls, no shifts are missed at all when testing the sequential shifter in the setup menu. It'll hit 1000/1000, up or down, all day long. The mis-shifts only happen while driving out on the track. This made me consider EMI from my DDW, but rerouting cables and using different USB cables and ports made no difference. I've also tried a few different sequential shifters and all have the same problem - even the 'sequential mode' on the Clubsport shifter falls foul.
Has anyone managed to find a solution for when secondary bindings and 'combine with keyboard' are needed, or is this one that Ilja must resolve? At the moment, using a sequential shifter is far too hit-and-miss to be practical.