Edit 2: And SteveLaw's point on page 2 of that thread is a pretty good one also. Where is he these days? Has he given up on us?
I'm not sure his point holds much water though. An intelligent species could interpret our signals without knowing the underlying logic or origin, or language. It would certainly help to have an outside reference - a human "Rosetta Stone" if you like - which conveys the same message in another form and/or with additional context.
For instance, if they observed ships tend to transit a certain signal sequence (... _ _ _ ...) when in trouble, they could reasonably conclude this is a request for help, and thus have learned that phrase, perhaps without ever knowing that it consists of 3 distinct letters, or that does letters are S.O.S., or that those letters are not an acronym for anything. There's no reason they would have to be able to speak English (or, indeed, any human language) in order to communicate with us via Morse.
Still, I think we're nearing a dead-end, I don't think there's much in there other than maybe the nearest system. It's nothing to do with the above - it's much simpler. If you look at the incredibly buggy nature of the career progressions, and frequently broken mission text, and copy 'n' paste nebulae, and simplistic & repetitive gameplay - do you really think Frontier spent a lot of time hiding a complex puzzle in Morse in multiple broken soundbites in containers hidden around the Galaxy?
Don't get me wrong - I love the game. But I'm afraid we're putting a hell of a lot more time, effort and imagination into this enigma than Frontier are/have - so far at least.