WebXml (http://svn.apache.org/repos/asf/tomcat/tc7.0.x/trunk/java/org/apache/catalina/deploy/WebXml.java) and in ApplicationJspConfigDescriptor (http://svn.apache.org/repos/asf/tomcat/tc7.0.x/trunk/java/org/apache/catalina/core/ApplicationJspConfigDescriptor.java) jspPropertyGroups are HashSet but this kind of set doesn't preserve the order in which elements are added. However it should be guaranteed to be spec compliant. Using a LinkedHashSet instead of the HashSet fixes this issues.
Thanks for the report and the suggested fix. Trunk and 7.0.x have been updated. The fix will be in 7.0.24 onwards.