Hello, Consider that you just received five new messages; you go to 3d message, read it and hit Delete to delete it. You're expecting focus to go to 4th message. Instead Claws Mail jumps it to 2nd one. I did not experienced this in my previous installation. It was again under a Debian (jessie), while this one is under Siduction. I'm assuming that this has to do with Claws Mail.
There is a hidden option, 'next_on_delete', which controls exactly what you are talking about. You have that set to '0', change it to '1'. This is documented in the manual and was detailed in the release notes.