Internet working behind proxy LAN in new El Capitan

I have created Question here to explain the full issue,

http://superuser.com/questions/991937/system-proxy-settings-not-working-after-up dating-to-el-capitan10-11-1

Have contacted Apple Support but they are also not able to figure out what is the issue,

I cant leave proxy as in my office all network is only in proxy.

This was working fine before i have updated to El Capitan and not suddenly its stopped working,

Still same proxy is working in Firefox but nowhere else.