Hi Shag - I didn't find Mission 1 too hard, and if I had to guess where you went wrong: Did you distinguish between half- and quarter-notes? Quarternotes are a "dot", half notes a "line", and breaks separate the letter. Let me know if that helped any!
couldn't find anything in the forums, so I'm just going make a new thread. I found this armchair treasure hunt "Undercover Job" (Startpage | Undercover Job) which is kind of about secret agents and messages hidden in music. Has quite a cryptographic feel to it.
Anybody played it...