Matrix writes content to the DB and that is used in the admin and edit interfaces. An additional file is written out on the file system to save on DB queries for page loads. It is also used when safe editing; allowing us to store different content in the DB and on the file system.
This implies a permissions error on your filesystem (i.e. that Apache can't write out that file). You should check that Apache and the Squiz Server (if you're using it) run as the same user to reduce potential permission conflicts.
Everything needs to run as the same user: Apache and the Squiz Server (Matrix obviously uses the same user as Apache does). Also, remember to use the Apache user's crontab for the Cron Manager script and Bulkmail script.