The Scenery Object Library must be below the added Rwy12 scenery you've added.  Did you move the newrwy12scenery.bgl file to your FS9 Addon Scenery folder?

I think what wji is referring to is the hierarchy setup in FS itself.  When you add new scenery, the list that is created (where all your addon scenery is listed) tells FS which scenery stuff to load on "top".  This translates to:

If you have two airports at the same location, FS will place the one closest to the top of the list (highest "priority") instead of the one set at a lower priority.  To fix this, go to the scenery screen in FS and highlight the Runway 12 section.  Click "Move up in list" (or the nearest equivalent) and get it above everything else.

OR

He's referring to the list in the actual scenery.cfg file in the main FS directory, of which I have very little experience editing.

As for the Runway 12 stuff, you must make sure that it is set up cleanly.  When you export from Rwy12, it should give you a dialog box saying the relevant BGL file was created.  Make sure you also save the XML file, so that you're able to edit if need be.  Then make sure the file is ADDED to FS.  Everything must be added correctly, or FS will not register it.

I had a similar problem with my first airport scenery.  My problem was too low a scenery density in the FS9 setting.  The higher densities, of course, cost you frames per second.