Kile 2.0: "cd .. && make" was a valid command in Tools menu, everything works fine as expected.
Kile 2.0.82 (Ubuntu 9.04): "cd .. && make" does not work at all, I still can run this tool but nothing happens. I workaround it by createing shellfile "/usr/local/bin/cdup_and_make" and running it instead.
Possible clue: When running this tool (cd .. && make) with "Running in Konsole" setting I got an error "diagnostics: no 'cd' command in you path" (or something like this). It looks like rather stupid diagnostics for me.