The syntax %{REQUEST_FILENAME} is slightly obsolete and should be replaced by %{DOCUMENT_ROOT}%{REQUEST_URI} for Apache 2.2 or better, which you are probably using. This change wouldn’t explain the the error you are seeing, however.
Out of curiosity, what happens if you use an absolute path for the rewrite?
RewriteEngine on
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} ! -d
RewriteCond %{DOCUMENT_ROOT}%{REQUEST_URI} ! -f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^(.*)$ /index.php/$1 [QSA,L]