Do you have anyother plugins installed? Like Better WP security or any others that write to htaccess?
To see if its acutally W3TC that rewrites you can when the sites is running fine, when htaccess has been rewritten by W3TC, go to General Settings page and towards bottom you find, "Verify rewrite rules", uncheck that box and save. This will prevent W3TC from writing anything so if it still fails its not W3TC.