I guess my next question is, what kind of system is it, what control panel, OS, and is it a dedicated server or VPS, and if it is a VPS, what kind of VPS technology. On all the systems I have worked with, I can login via SSH as root, and edit the hosts file as needed. If nothing you have done should have made those entries, then you may have some root hack issues. Check the logs, and perhaps install a root-kit checker.
I have yet to run into a situation where the information in the /etc/hosts file was not something I could have predicted.