Inspite of changing passwords and all the other stuff I did, the file is modified again. My auditor crawls the directory comparing file checksums and permissions...
From the (now) hourly audit:
*** File Audit Results ***
['*.php', '*.html', '*.py', '*.cgi', '.ini', '*.js', '*.inc', '.htaccess', 'favicon.ico', '*.pl', '*.htc', '*.css']
<br>
<br>
File contents changed. 1<br>
/home/*****/public_html/manager/frames/nodes.php [-564478809 100444]
If there is malicous code on my website it was in place before the auditor was installed (July 4th) or it is code somehow injected in to the database. I now know the the fle change happens between 23:00 and 00:00 hrs (Server time). The 100444 above shows that the file has been left as read only so whatever is doing this is changing the access to manager and frames and nodes.php to write access, modifying the file then changing them all back to read only.
For comparing notes - I am running MODx 1.0.0, SMF 1.1.10, Gallery2. Apache 1.3.41 (Unix),MySQL 5.0.67-community.
I am going to remove Gallery2 temporarily from my site as I see many alarming things in the Error log.