Thanks guys, I managed to fix the issues here, apparently I was using the wrong version of a few specific sceneries. I did a complete uninstall/reinstall and now everything is showing OK.

There is a somewhat different twist in P3Dv5.x regarding removal of default objects to prevent conflicts with scenery designed for P3D v4.5 and earlier.

P3Dv5 default sceneries often include new autogen objects in addition to standard scenery objects.  If you load the stock airport into ADE, mousing over the various default scenery objects on the airport will show a description, and if any of the objects are autogenerated, simply placing new exclusion rectangles into your add-on's airport file (e.g. ADE/AFX) isn't enough to get rid of them in v5.  You have to create a separate set of exclusion bgls--you load the stock scenery into ADE, place a/an exclusion rectangle(s) that cover all the autogen objects you intend to remove, then delete everything except the runways, navaids, and the exclusion rectangle(s) you just created.  Compile that and place the resultant bgl files (there should be a cvx file as well as the airport file) into the scenery library in a separate new layer below the add-on you are modifying.  That will remove the stock autogen sceneries.