I was running this Wordpress install on Multisite, I have since removed multisite and put it back to a single site installation following the correct procedures.
Since then I have had this issue with W3TC so uninstalled the plugin completely and did a reinstall in the hope that would resolve things but the same issue is still occurring. The issue is that upon activating and saving config options for W3TC my site gets a 500 server error instantly, the problem is that it seems to malform the htaccess file by either not completing the W3TC rules correctly or it simply duplicates the original wordpress rules many many times. As soon as I reset the htaccess back to the default all is okay but I can't seem to run W3TC anymore because of this bug and I really need to use the plugin on the site.
Any ideas if there is anything I need to do as a complete remove and install doesn't seem to have resolved things for me on this