Transparent Diffuse doesnt work after lightmap

Hey, guys I am using a script to make my objects auto transparent when the camera hits the objects. It was working fine in 3.5.7.. recently I ugpraded to 4.2.1 and I noticed that transparency doesnt work after lightmapping. If i create a new project to test, it worked. but transparency doesn't work in my game after lightmapping.

Please tell me what I should concentrate on... I am not using any custom shader , i Use the shader provided by unity and my script is a simple script which converts the shader selected to"transparent/diffuse" from "diffuse"

The funny part is the script is working, i see the shader change in inspector along with the chagne in alpha channel, but visually it doesn't work after i finish baking the lights. please help

Thanks a lot for ur support in advance.