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looks like it is Hydrogen that is not playing right when asked to save its command under JACK session request.

as a matter of fact it is hydrogen that's missing to prefix the filename in its command line arguments with "${SESSION_DIR}", literally as required by the JACK session protocol spec--that is in your example: "${SESSION_DIR}Klen.h2song".

so please ask the hydrogen devs to fix the JACK session callback procedure as it is not a qjackctl issue per se.

cheers