I think I got to the bottom of this. It feels like there was a problem with my board - I started to test the RC exclusive-or gate (U1203 74LVC2G86) as I was suspecting something’s wrong with it. I clean it up and it started to work!
Now the pixracer recognizes all the signals but I still need it to recognize an inverted ppm.
Is there a way for pixracer to accept inverted ppm-sum?