apauto,
Like Tommybs said, something else may be at work here, and it's probably a good idea to follow up with his advice about FTP accounts and server logs.
XSS - cross-site scripting accounts for the majority of website mangling that happens. Javascript can certainly be a security vulnerability if form fields and textareas aren't cleaned and validated. It's best to be aware of character input which might slip by validation scripts. Event handler attributes are also used since several browsers allow characters between the handler and the equals sign.
A few often-overlooked security holes are input fields and the browser's address bar.
If inputs don't have both client-side and server-side validation, a "hacker" could submit scripts to your server with simple form submissions...and not necessarily Javascript...these attacks can be written in many languages.
Modifying the URL query string in the browser's address bar is often a problem. PHP's $_GET superglobal retrieves values which are set in the query string need to be validated and "cleaned" of special characters to limit input.
SQL injection is a common mode of attack. Appending SQL commands with a semicolon ";" after the id's value will be executed if the SQL query is simple:
http://www.example.com/index.php?id=23;insert into table ...etc.etc.
The injection starts with the semicolon:
$q = 'SELECT * FROM table WHERE id = ' . $_GET['id];
Your script expects $_GET['id'] to be '23' or something similar, but instead it is something like:
23;insert into table ...etc.etc.
If you write SQL with command line, you'll understand this a little better.
Header injection exploits CRLF (carriage return, line-feed) characters and injects foreign code by remotely modifying HTTP headers. It's quite frightening how many websites are vulnerable to this.
If the code on your host uses includes or requires (include();require();) based on GET or POST variable input, then someone could modify the value of form inputs with Javascript, and create havoc on your server.
I won't post all the methods I know of, but this should help you track down what sort of fix(es) you need to employ.
You can find several good Javascript form field validation scripts, along with server-side validation scripts which will clean up any malicious code before it can be executed on your server. Additionally, you should probably look into XSS and how to protect against it.