Does anyone have problems using the automated passport gates when leaving Japan?

I have a British passport but whenever I use the automated passport gates leaving any airports in Japan (so far I’ve tried HND, NRT, KIX and CTS), my passport does not work with these automated machines and then I get redirected to the manual line. This is incredibly frustrating as the manual lines can be long (I’ve seen only one counter is opened and usually families with children occupy the entire queue). I tried asking the officer in CTS when I got redirected to her to be “stamped” instead, but she didn’t understand English and basically ignored me…

I wonder if anyone else has a similar problem and how did you resolve this (if it’s even possible)?