1) Did you placed your menu inside a4j:include and using navigation? Or your a4j:include el-binded to some page adress through the bean and jsut reRendered?
In general it'll be better if you paste your code(main parts) and explain what have you achieved and what you want to change.
2) menuItem - in server mode works the same as standard command link.. So if you still want to change the code to use real frame and links in menu - it should works ok.. should be also examined additionally with your examples.