Narrowed it down to the shaders folder in the common folder.
It's one of these or all of them
db
dcl
win32_30
win32_30_atidx10
win32_30_low_ati
win32_30_nv6
win32_30_nv7
win32_30_nv8
preload.list
When I used the vanilla folders of those 9 above, lightbars are no longer transparent. Now I'm gonna add 1 by 1 and see which folder(s) are causing the problem.
UPDATE:
So I replaced each folder one by one and when I got to folder win32_30_nv8, that's when I noticed that the lightbars become transparent!! Now which file could it be?
UPDATE 2:
Went through the win32_30_v8 folder and came across "gta_vehicle_vehglass.fxc". That appears to be the culprit. Once I switched it with vanilla gta_vehicle_vehglass.fxc, the lightbars are no longer transparent.