What's the difference between a flight recorder and a black box?
No difference, but since the Starcub was itself an autonomous vehicle, designed by the fine folk at Lockmart™ ( "Your Mission is Ours!"
®) to operate independently whether associated with a mothership or not, one could presume that the Narcissus has it's own flight recorder, separate from the Nostromo's. but they were likely sync'd with each other.
[...] are we to assume the message somehow got sent onto the company Intranet and was retrieved from there? If that's the case what too so long to get it and why did Amanda have to go to the station to get it?
I think it's safe to assume the SOS message got sent over Network, and maybe some bits of telemetry and the initial transmissions from when they made system fall, but as to how or why that data was subsequently lost or buried is a compelling question indeed, one I think could be best answered by whomever was pulling Ash's strings.
Any physical recoveries from the wreckage of the Nostromo would have been a loose end in need of tidying asap, hence the immediate company dispatch, the only gum in the works was Samuels' sympathies for Amanda's story and all the trouble her inclusion on the mission brought about. friggin robits.
Regarding the recovered data, presumably Marlowe and Ransome had to do some digging in order to recover what they did from old server backups and local communication buffers.
[...] It's entirely possible the message was floating out in space and they simply couldn't find the Narcissus.
And we all know Why they couldn't find the Narci, right?? Because Buddha fakkin' Robits. That's why. There's gotta be some greasy ICC palms all across the core keeping these things Roving about, wild and free. Gods'bless the sweet capitalistic freedom of the international skies; exploiting that tasty manna from the Middle Heavens. Mmmmn-Hmn.