This thread is month and a half old, yet I'm still having described problem.
I decided to disable machine, killed Kraken, came back to Fleetmaster Okaya but no conversation with her can be started.
-------------------[edit]--------------------
If anyone is looking for solution/workaround - starting the quest again (thankfully I had some save before landing on Sayuka) helped me too. In the run I got the bug I was checking every of three pylons before even going to the main machine. This time, as I wanted to help RDC, I didn't even touch these pylons, just went straight to the main machine and disabled it the moment I was able to. Killed Kraken and this time I was able to proceed with quest by talking with Okaya.