Apache On the Fly Configuration Changes

I'm in trouble because my Apache Server is adding Javascript code just before closing head tag. I tried to find out but could not success what is going here on the server. When I restarted the server then it went away, but after sometime I'm facing same issue. I'm sure my server is compromized and someone is playing with apache which is then doing change in the delivered content. I'm running Apache/2.4.6 (CentOS).

I know we can confiugure Apache to change the content before delivering it but if this is the case then how restarting Apache is loosing that configuration. Though I have tried searching all the configuration and I could not find any such entry in the configuration file.

Kindly help me on this, I will really appreciate your time and effort in getting my problem resolved.

Thanks in advance.