I assume you installed this without Slat's LC-39 EAFB 2006.3- Hi-Res? If so just try changing the default Canaveral CFG base coordinates from this:
Location = -80.675 +28.5208
to
Location = -80.672 +28.528
If I remember correctly this will offset the runway slightly unless you use Slat's Add-on but will fix the lights.
A word of caution, if you install Slat's add-on & High Res KSC the surface tiles will overwrite the LV14 KSC tiles in 2010P1 if you installed those.
or try this:
This is from Slat's LC-39B scenario which uses Brian Jones' Lights:
POS -80.6208830 28.6271200
HEADING 2.00
Hope that helps.