You can replicate this issue by building an U shape with wall blocks (3 wall blocks in a row and one block on top of the first and the last one) and then fill the gap with another wall block.
If you build the wall in north-south direction, you will get a flat wall.
If you build it in east-west direction, the lower block will be updated to the non flat version (up: true).
Confirmed for 18w01a, no entries appear in villages.dat.
You can replicate this issue by building an U shape with wall blocks (3 wall blocks in a row and one block on top of the first and the last one) and then fill the gap with another wall block.
If you build the wall in north-south direction, you will get a flat wall.
If you build it in east-west direction, the lower block will be updated to the non flat version (up: true).