it looks to me like ET is using the wrong lightmaps… are you sure that bsp -meta, bsp -vis, and bsp -light -fast compiles without any errors?
bsp -meta -vis - light -fast -filter (from the radiant menu) does all these 3 steps for you… if it stops at any of these stages, please post the log. my first guess is that you have a leak or something like that and that you are loading an old version of the map with different light maps.
you can also have a look at the file dates of yourmap.bsp and the lightmaps in the folder yourmap*.tga… the tga-s should have a slightly newer file date than the bsp.
BTW: you really should use q3map_lightmapMergable for terrain… it saves you a lot of texture space.
EDIT: one more thing: did you build a .pk3 for your map recently? in this case the bsp from the pk3 is taken… which of course does not match with your new lightmaps… therefore, (re)move this pk3.
EDIT2: oh, i see, that you already placed lightmapMergable in your base shader… ok, then forget about that… but AFAIR you have to place the base shader on top of all other terrain shaders… so just move the last shader to the top of your shader file.