When I view the tomcat source code at http://grepcode.com/file/repo1.maven.org/maven2/org.apache.tomcat/tomcat-catalina/7.0.0/org/apache/catalina/connector/Request.java#Request.
First, let's use a more recent version of Tomcat. 7.0.0 is years old: Request.java from Tomcat 7.0.34
Second, the parseParameters method does not set the encoding: it fetches the encoding which has been set by other components. Some places where the content encoding might have been set:
If you just want to set the URI encoding to UTF-8 unconditionally across your site, then just use the URIEncoding attribute in your 
The direct answer to your question is that server.xml's URIEncoding attribute does not work in this method: it works elsewhere.