Step File Export Error

We’re using KiCad to lay out a large board and we rely on the 3D models for aligning our PCB to the enclosure. We’ve run into a strange bug where the step export in an old version “extruded” the PCB down from the existing 3D models but in the current version it appears to extrude up. This leads to inaccurate heights and interference between the board and objects on the board. See the images below for what I mean.
The PCB here lines up with the connector above and diode below as expected:

The bottom of the PCB is now where the top should be and the board volume interferes with the connector model: