Ugh, again i have to resurrect another thread. I'M SORRY.
I wanted to update this because i fixed the issue, and if someone else has this problem i want them to see the solution here.
Basically, you have to keep in mind that your materials work in a little hierarchy as well. When you map your new ELS lights, you need to make sure that the ELS lightsemissive material is ABOVE the vehglass material for your windows (if it's a slicktop) or your lightbar's glass.
If you, like myself and i'm sure many others, find that your lightsemissive material is below your vehglass material, all you have to do is copy the vehglass material. the new vehglass material that is created (don't forget to rename it! duh!), will be at the bottom of the list. After copying it, apply the material to the vehglass that you cannot see your lights through.
Good luck!