Raynes Park – Amersham, and Dartford – Brentwood is £6.20 peak, but Brentwood – North Dulwich is £8.30 peak. All are Zones 2-9 mixed-mode journeys, however, Dartford – Brentwood and Brentwood – North Dulwich involves an Anglia route.
Also, Chesham – Cheshunt is 2-9 TfL with Anglia but the fare charged is the same as 2-8 Anglia, rather than the 2-9 Anglia fare.
The somewhat clumsy add-on of different fares for Anglia, at the insistance of the DfT, causes quite a few anomalies. I’m considering dropping the 7-9 rows from the table because it’s notoriously difficult to describe the permutations succinctly. One of the biggest issues is whether NR or Ang takes precedence. One of the flows I use to create the table (Cricklewood to Brentwood) has changed a year ago.
As to your issues, In the case of Dartford to Brentwood (which is actually 3-9) I think the fact that Dartford is beyond zones 1-6 is trumping the Anglia fares. North Dulwich isn’t outside zones 1-6 and so is subject to the Anglia fares. Chesham (and Amersham) to Cheshunt is treated differently because the expensive end is Cheshunt in zone 8. Anglia fares are set for zones 7-8 for Theobalds Grove, Waltham Cross and Cheshunt, and zone 9 is just for Brentwood.