I wanted to get below 1 minute for E1M1 so I played the game bit different than before and recognized this:
I have run toggled on, then after falling in E1M1 I crouch into the ventilation shaft. When I'm into it I cannot kick with fire-key, I see the crosshair wobbling but nothing happens, only the kick key Q works. Behind the shaft, when standing, the kick works again with fire-key or Q.