I have looked at REX and cannot find anything that I know of the is interfering
If it has replaced some default textures, that explains why they changed colors, and they surely have. Maybe it wasn't REX, but something else you installed long ago.
I have uninstalled JFK and re installed but again the same problem.
If the 3rd party product that has replaced a default effects textures that is used by JFK (and probably by other sceneries too), reinstalling JFK won't change anything, because it's not something that is part of JFK installation.
Really not sure which 3rd party add on is causing the textures not to display correctly, appreciate any more offers of help
I don't have any more clues than you, nor I can possibly know everything that you installed but, as I've said, the issue is caused by some files or textures that has been replaced in the DEFAULT FSX\Effects folders, either by another add-on installer, or you might have installed it manually long ago and forgot about it.
The problem is not a JFK problem, if something replaces a default Effects file, ALL your sceneries (both default and 3rd party) that calls for it, will be affected as well.