Markoz wrote on Jun 6^th, 2012 at 2:22am:

Hi Jason. I did a repair of FSX to fix my problem with the red and green NAV lights on ALL my Captain Sim aircraft. I believe that I uninstalled a 3rd party addon ( don't know which one) and it deleted the red and green NAV light FX files on me. After the repair, they were all there again. ;) Mark

My NAV light colour issue came from 3rd party software. A weather related
software with textures.......... ;) After a reinstall, the colours and lights came back.