It's likely a bug in the scenery editor, the compiler, or the sim.
The runway start positions have a "PRIMARY" and a "SECONDARY" tag in the scenery source XML so, in theory, it shouldn't matter in which order they are listed there, the sim should always recognize which is which.
However, if you edit the start positions and for some reason you start with the secondary one, it IS correctly flagged as "SECONDARY", but it appears in the source file *before* the primary one, just because you edited it first so, it seems the simulator ignores that tag, and always assume the start positions that comes first is always the primary.
So, we just swapped the two lines, and the problem is fixed, but it was clearly a simulator bug which ignores the runway start primary/secondary tag, since the very existence of the tag is precisely to allow to define them in any order, if it worked.
You can get the update now from the FSDT Live Update.