It's not clear whether you are using the code I recommended or not...
Delete (or comment out) the two rules in /app/.htaccess. They should not be needed at all, since these requests are handled by the rule in the /.htaccess file.
The code in /app/webroot/.htaccess can be improved for performance by excluding all filetypes that the "index.php" script cannot generate. For example, there is no need to check the hard drive for 'file exists' if the script cannot create an image file or a css stylesheet, or a PDF document. The more filetypes excluded, the fewer times the server will have to read your disk. So, for example, in /app/webroot/.htaccess:
RewriteEngine on
RewriteCond $1 !^index\.php$
RewriteCond $1 !\.(gif|jpe?g|png|css|js|doc|pdf|mp3|swf|flv|mov|wmv|avi)$
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ index.php?url=$1 [QSA,L]
It is not critical to exclude *all* filetypes that the "index.php" script cannot create. It is only necessary to exclude the most-frequently-requested filetypes. The 'list' I show is just for illustration, and you should adjust it to suit your site.
The code appears to assume that the "index.php" file is located at /index.php and not at /app/webroot/index.php. Is that correct? If not, adjust the exclusion patterns and substitution paths.
Also, The <IfModule> containers are a waste of CPU time unless
you want this code to fail silently on servers where mod_rewrite is not available -- rarely the desired behaviour.
Jim