Hello,
I previously had a texture issue with CYVR where REX replaced the file and made the runway look darker. That was fixed by doing a reinstall.
Now, i recently moved to Windows 8.1, and i have the same issue. This is a clean install with just P3D V3.1, CYVR and GSX. No other addons have been installed and i have a similar issue. Also, i did click yes on update AFCAD.