I used to have this happen for a few years, following my passport having been stolen and getting a new one. Maybe border guards get some kind of message when someone like this shows up.
I’ve had this experience two times. My wife was able to see the border agent’s screen and told me the agent was comparing my pictures to pictures of criminals. So it takes a while, because the agent has to compare you against lots of faces. Maybe there’s more to it, but I think this is what takes long.
Happened always to me here in Tw before I could use egate. This is because the bio data page got a slight crease (I’m a bit messy…), So they always check if it was counterfeit or not