The META-INF/services/java.nio.charset.spi.CharsetProvider file is ignored by the container. If the charset extension classes are placed lib/ext of JDK then the charset extension is available everywhere except in the web application. It can be a improper class loader problem in Catalina.
Your Charset should be loaded by the bootstrap classloader providing it has been placed in $JAVA_HOME/jre/lib/ext as per http://jakarta.apache.org/tomcat/tomcat-4.1-doc/class-loader-howto.html Have you placed your jar in the correct directory?
Since there has been no response to my previous comment I am going to assume that this was a configuration/file location issue and therefore resolve this as invalid. If this is not the case, please re-open the bug and if possible provide a test case that demonstrates the issue you are seeing.