I really loved this story. I know this thread isn't really going anymore but I just wanted to throw my thoughts in having gotten to it late.
I understand why people could find it convenient that Duxa had endless resources to fix the problems she encountered and I can appreciate the logistical questions of how something like Duxa could be built in the first place.
To me the story wasn't so much about these aspects of the universe the story is set in. I felt the author did a good job of setting up a scenario that leaves us with interesting questions. Humans in Duxa's universe obviously are more technologically advanced than us by a great deal, the plague didn't hit in any near future to us. Likewise, humans still manage to get wiped out. So we weren't masters of even our own solar system yet apparently. I felt enough information was given there to get us going with out having to give a step by step of how we got to where we are.
Earth has been rendered uninhabitable by a plague.
Our only choice is to engineer a new home in another system.
We used every scrape of resource we had left to create Duxa.
The real story here is only focused on the Sci-Fi in so much as it shapes who and what Duxa is. How she goes from something that only barely grasps death to truly understanding the value of life.
I found the scene when she kills Sun in freezing experiments to be right at the heart of this story. Even though the character exists in the story for just a little while, you get the feeling that Duxa has made a huge emotional connection to the him and she's really, for the first time ever, experiencing true loss.
Duxa had known people before, but I'd venture that Sun was the first real friend she'd had. To go from casually holding her sign informing everyone "I'm going to destroy your planet soon" to her outburst over Sun... well I found it very effective.
As for the inconsistent computing power of Duxa, all I know is my computer can do somethings nice and fast and other things painfully slow. I imagine a moon sized space craft which isn't even sure where it's own processors are might be just a tad inconsistent at times.