There has been an increase of script injections within your shared hosting environment, i had one of my sites where they added custom scripts to all my .js files, and another time when scripts were added to all my .html files. it would be great if in your findings you can share to the vps community this situations and solutions to prevent or solve issues so that we can keep our vps clean and safe. maybe a new forum about it or just post them in the forum.

reactorjay, there are a number of causes for this type of problem. Unfortunately some investigation is required to determine what the cause was in your case.

If you submit a support request we can look into it, but here are the most common attacks:

1. XSS - http://en.wikipedia.org/wiki/Cross-site_scripting
2. SQL Injection -> http://en.wikipedia.org/wiki/SQL_injection
3. FTP Compromise -> http://www.securityfocus.com/brief/966
4. Upload compromise -> http://www.acunetix.com/websitesecurity/upload-forms-threat.htm

Unfortunately you need to be pretty well versed in systems administration in order to pin point every vector of attack. In the event of a compromise your best bet is opening a ticket up with support describing the symptoms of your problem, at which point we can investigate your server to help track the source of the problem.

While we cannot make code changes for you, we can offer suggestions on how to secure your applications.