They were all working properly . I am 99% sure that the invisible ones are my customized ones. I also have no staircases.
Make that 100%. If installed the Paintkit, you must update that one too.
Note that, if you install it over your repaints, it will overwrite all your custom SIM.CFG file containing your customized [fltsim.xx] sections. But it MUST to that, since the sim.cfg must be updated.
If you want to save all the hassle of redoing your custom SIM.CFG, follow this procedure:
1) BACKUP all your _USER folders (assuming you added your repaints to the _USER Simobjects, which is the suggested way) into a safe place.
2) Install the current PaintKit
3) With a text editor, Copy & Paste from each of the SIM.CFG that you *backup*, all the lines from the [General] section up to the end of the file to the NEW SIM.CFG the PaintKit has just installed.
Note that, the updated PaintKit contains more repaintable vehicles, so after doing this, you might want to add your own [fltsim.xx] section to add your repaints to the new customizable vehicles too, paying attention at the airport assignments and naming conventions.