OK, played around some more and realized none of the options (such as showing/hiding the static C5 Galaxies) are actually taking effect. The .ini file gets updated with the appropriate lines, but the sim isn't actually enacting the changes.
edit: Actually it seems all FSDT sceneries I have are not reading the settings properly. KSDF for example, turning the ground traffic on/off isn't reflected in the sim. Again, it changes the ini, but the sim does not reflect the changes.
Forgot to add this is affecting FSX-SE and P3D v4.4 .