Lots of people seem to think the answer is on another planet, but we haven't even worked out the one we have yet! Michael has confirmed that Solo isn't bugged, and Open is showing more than it should. It's logical to conclude that obelisks in open are being activated by a process that we don't understand, due to the number of active commanders doing random things. What we need to apply ourselves to is how we are getting more active obelisks.
Scan an active obelisk and we get two things:
One: From Ran either an "intrusion" message, nothing, or decoded data. This depends on the contents of our cargo.
Two: Alpha-Epsilon data patterns.
The obelisk then goes inactive. Even in open, it's not scannable again by the same commander, which is a big pointer that Solo is not bugged.
Since MB has confirmed this is correct behaviour, and FD requiring a relog to progress is VERY unlikely, it seems likely that we need to progress using the only scan results we reliably get: The Alpha-Epsilon data patterns. I think we need to use these to somehow activate additional obelisks to scan.
Once we know the mechanism for activating obelisks, we can progress.