The "top" of a wooden log is rounded to an octagon, while the "body" of a log is rounded to a hexagon, making the place where they connect display with missing polygons. Seems to affect all of the logs that are rounded.

It seems that the issue resolved itself somehow.

This has to do with the value nVidia in the config.
You have to set this value to true if you have an Nvidia GPU, as there are differences in how they render stuff, and I haven't found a way to reliably set this at startup.
It's possible you accidentally set this value, and the problem went away.