Jeff,
Very strange issue that no one else seems to have including me. A few ORBX PFJ objects should be there (as you say) when you turn off Yes Bay. However, the missing trees seem to all be from vegetation_fsxrtm.bgl objects placed by the PLC_78K_Yes_Bay_Lodge.bgl which is the same .bgl that places the lodge and the ugly brown object that represents dirt as well as some trees and bushes from vegetation.bgl. You seem (I have not checked every object) to have everything in your pic from that PLC_78K_Yes_Bay_Lodge.bgl but the vegetation_fsxrtm.bgl objects.
The trees should appear unless the standard vegetation_fsxrtm.bgl is not available in your P3Dv4\Scenery\Global\Scenery folder. It is a standard file but is it possible for some reason that the vegetation_fsxrtm.bgl file is missing or deactivated on your system?
rgerdes,
The correct dates are 2012. Not sure how your dates got changed. You are referencing the old version of Yes Bay which had an upper and lower folder. The new v2 version does not since the upper folder only contained object library information. That information has now been consolidated into the new Part IV libraries. When you put the new Part IV libraries in, then you need to remove your old Yes Bay version and update to V2 of Yes Bay.\
Rod