I created 5 2-sided opaque facets to separate two regions of my vacuum system (memorized as vacSeparator), but in the simulation they act as transparent. To trouble shoot the problem I created a large square facet (#1623) that completely interects the main vacuum region. When facet 1623 is overlaping the vacSeparator facets at the origin it also acts as transparent, but when it is moved elsewhere it is opaque. The only change made was a move action. This is completely bewildering me. I've uploaded two simulations with facet 1623 in two positions and textures to show the pressure when is side view. There is only outgassing on one side of the system.
You have a planarity problem: Molflow assumes all facets to be panar (all vertices in the same plane). When you choose Selection/Non-planar, six facets (five of them part of the vacSeparator) will be identified as non-planar. You can check when you press the Details button on the right: the planarity column shows the largest distance of a vertex from the facet's plane. Also, displaying the normals show that something's not right:
Click for larger view
The facet's plane is determined based on the first three indices. When you perform a move command, it is recalculated, therefore the planarity was probably better (still not perfect, some molecules could cross the surface).
To fix planarity, either you have to redefine the surfaces from scratch, or use the Facet / Project command to project all vertices to a known plane (easy in your case since your surfaces are oriented towards the X,Y,Z axes). I attach a fixed example.
Hint: the easiest to fix a non-planar facet is to select three vertices on it then use the Project command with 3-vertex plane definition mode. When doing this, you can save time by holding TAB to switch between facet and vertex selection modes, and CAPS LOCK to restrict selectability of vertices to selected facets and vica versa.