.htaccess - RewriteCond: bad flag delimiters

Since you know that the problem is with a RewriteCond, you can locate the problem rather quickly by eliminating half of the conditions and then test the remaining.

You can start by removing the first rule. The error remains. As the next step remove the first half of the remaining RewriteConds (about 20) and test again. Proceed until you reach a handful of RewriteConds and remove them one by one.

The error disappears with the next to last rule. Reinsert this rule to verify, that the error appears again. Now look at

RewriteCond %{QUERY_STRING} (;|<|>|'|"|\)|%0A|%0D|%22|%27|%3C|%3E|%00).*(/\*|union|select|insert|drop|delete|update|cast|cre ate|char|convert|alter|declare|order|script|set|md 5|benchmark|encode) [NC,OR]

What's wrong with this condition? Do you see the spaces in cre ate and md 5?

As soon as you remove these spaces or escape them with a backslash \, the error is gone.

There are some (probably) unwanted spaces in the regexes, this is working for me:

ServerSignature Off
Options -Indexes

RewriteEngine On

RewriteCond %{REQUEST_METHOD} ^(HEAD|TRACE|DELETE|TRACK|DEBUG) [NC]
RewriteRule ^(.*)$ - [F,L]

RewriteCond %{HTTP_USER_AGENT} (libwww-perl|wget|python|nikto|curl|scan|java|winhttp|clshttp|loader) [NC,OR]
RewriteCond %{HTTP_USER_AGENT} (<|>|'|%0A|%0D|%27|%3C|%3E|%00) [NC,OR]
RewriteCond %{HTTP_USER_AGENT} (;|<|>|'|"|\)|\(|%0A|%0D|%22|%27|%28|%3C|%3E|%00).*(libwww-perl|wget|python|nikto|curl|scan|java|winhttp|HTTrack|clshttp|archiver|loader|email|harvest|extract|grab|miner) [NC,OR]

RewriteCond %{THE_REQUEST} \/\*\ HTTP/ [NC,OR]
RewriteCond %{THE_REQUEST} etc/passwd [NC,OR]
RewriteCond %{THE_REQUEST} cgi-bin [NC,OR]
RewriteCond %{THE_REQUEST} (%0A|%0D) [NC,OR]
RewriteCond %{THE_REQUEST} \?\ HTTP/ [NC,OR]

RewriteCond %{QUERY_STRING} ^(.*);(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} ^(.*)\"|\(|\)(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=http:// [OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=(\.\.//?)+ [OR]
RewriteCond %{QUERY_STRING} [a-zA-Z0-9_]=/([a-z0-9_.]//?)$ [NC,OR]
RewriteCond %{QUERY_STRING} \=PHP[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12} [NC,OR]
RewriteCond %{QUERY_STRING} (\.\./|\.\.) [OR]
RewriteCond %{QUERY_STRING} ftp\: [NC,OR]
RewriteCond %{QUERY_STRING} http\: [NC,OR]
RewriteCond %{QUERY_STRING} https\: [NC,OR]
RewriteCond %{QUERY_STRING} \=\|w\| [NC,OR]
RewriteCond %{QUERY_STRING} ^(.*)/self/(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} ^(.*)cPath=http://(.*)$ [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^s]*s)+cript.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (\<|%3C).*iframe.*(\>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} (<|%3C)([^i]*i)+frame.*(>|%3E) [NC,OR]
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [NC,OR]
RewriteCond %{QUERY_STRING} base64_(en|de)code[^(]*\([^)]*\) [NC,OR]
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2}) [OR]
RewriteCond %{QUERY_STRING} ^.*(\[|\]|\(|\)|<|>).* [NC,OR]
RewriteCond %{QUERY_STRING} (NULL|OUTFILE|LOAD_FILE) [OR]
RewriteCond %{QUERY_STRING} (\./|\../|\.../)+(motd|etc|bin) [NC,OR]
RewriteCond %{QUERY_STRING} (localhost|loopback|127\.0\.0\.1) [NC,OR]
RewriteCond %{QUERY_STRING} (<|>|'|%0A|%0D|%27|%3C|%3E|%00) [NC,OR]
RewriteCond %{QUERY_STRING} concat[^\(]*\( [NC,OR]
RewriteCond %{QUERY_STRING} union([^s]*s)+elect [NC,OR]
RewriteCond %{QUERY_STRING} union([^a]*a)+ll([^s]*s)+elect [NC,OR]
RewriteCond %{QUERY_STRING} (;|<|>|'|"|\)|%0A|%0D|%22|%27|%3C|%3E|%00).*(/\*|union|select|insert|drop|delete|update|cast|create|char|convert|alter|declare|order|script|set|md5|benchmark|encode) [NC,OR]
RewriteCond %{QUERY_STRING} (sp_executesql) [NC]
RewriteRule ^(.*)$ - [F,L]

<FilesMatch "^(install\.php|setup\.php|wp-config\.php|config\.php|configuration\.php|php\.ini|php5\.ini|bb-config\.php|db.php)">
Order allow,deny
Deny from all
</FilesMatch>

Options -ExecCGI
AddHandler cgi-script .php .pl .py .jsp .asp .htm .shtml .sh .cgi
AddType text/plain .pl .cgi .php
<FilesMatch "\.(php|pl|py|jsp|asp|htm|shtml|sh|cgi)$">
ForceType text/plain
</FilesMatch>