Encountered the same game-breaking bug.  Not sure why since the trial quest had initially sent me to investigate the Overmind.  I'd gone to their homeworld and never even thought of Beta Chaudhary, since I wasn't aware of their presence beyond a crashed ship.

The problem seems to have sorted itself out, I loaded the game today for the first time since Sunday and just by reloading the save it has sorted out the problem. 

Thanks for the reply.

Huh........I'll tell you what is broken about that quest. The fact that you can open the Origin WITHOUT having progressed with the Phamysht. The Mu'kay won't continue the quest line once our freakish friends appear. There needs to be a blocker on the Origin doing it's thing w/o having first talked to the Phamysht successfully. Kind of ruined the game a bit for me. I'll have to restart before I visited that planet at some point so I can do the order of events properly. Kind of don't want to though...

Hey folks,

I've asked our designer to take a look.  I'll let you know what he finds out.  

We have a fix for the bug internally -- do you mind sending me your save game to verify?  Please send to pshaw@stardock.com

From our designer:

So here's what we think happened:

• You landed on Titan and examined the Scryve wreckage there.
• This marked complete the relevant Objective.
• Your lander died before it could take off. Lightning maybe.
• Internally, this caused the quest to not realize that it was "done."

We have an internal fix that do two things:
1) It's prevented new players from getting into this situation.
2) For you (and anyone else in this situation) the Objective has been marked incomplete again. You'll see in your Objectives log "Find the wreckage of the crashed Scryve vessel in the Sol system." Return to Titan, revisit the Scryve wreckage there, take off, and the quest should continue normally. Your next stop will be the Mu'Kay Homeworld.

For right now, you should be about to revisit Titan and the Scryve wreckage there, and everything should be cleared up.  

Sorry for the inconvenience, and thanks for reporting this!