Hi
Both version should be correctly stopped. pg_upgrade started clusters itself.
Please check pg_upgrade_server.log file in directory where pg_upgrade was run.
Also where is postgresql.conf? In PGDATA? Otherwise you need tell pg_upgrade 
correct path, for example with options '-o " -c 
config_file=/etc/postgresql/8.4/main/postgresql.conf" -O " -c 
config_file=/etc/postgresql/9.4/main/postgresql.conf"'

regards, Sergei

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