Wudgles--> I am a prior enlisted nuke who qualified as far up as an enlisted guy can qualify...
Two quick things:
1) My apologies for assuming you knew nothing of the NUKE life.
2) When talking about "life in X community", giving credentials ahead of time helps everyone out.
I was selected sailor of the year at my command and received all EPs as an E-6. I finished #1 in my class through all nuke schools. I finished #1 in my class through all nuke schools.
Not to throw salt on a wound, just giving my honest opinion: I would imagine that the STA-21 board thought your application package read "FUTURE SUB/NUKE OFFICER" all over it. Add in the 4.0 GPA in a technical major, I can see why the NUKE bubbas are probably going to snag you from doing what you really want to. Hopefully, you'll be able to pull some miracle out of your ass and dodge it. It's not impossible, but I've only seen one person do it (my previously mentioned buddy).
On the upside, at least you're not going straight SWO, which in my uneducated and inexperienced opinion would be a worse choice than NUKE (same miserable hours for the most part [non-academic] with much less compensation for it).
Good luck to all the FY'11 middies, both in service selection and not getting hosed by IRR.