As a successful applicant this year I can add some information. (By the way, I was an unsuccessful applicant last year). I received a phone call the week before Memorial Day 2011 letting me know I was "recommended for funding". There appears to be several steps, only some of which are transparent, between "recommended for funding" and "funded". I had a some forms to fill out and files to upload, including a letter from my adviser stating I had satisfactory performance academically and in research, and that my research topic had not changed significantly from what I submitted with my application. This paperwork had to be complete by June 3, 2011. Next, there are a series of steps the EPA needs to take, including a 5 business day hold on the award letter. This places the absolute earliest of the award letter reaching me to be June 10th, and more likely sometime around the middle of the month. Very possibly longer, considering how things have been dragging out this far.
The steps between "recommended for funding" and "funded" are detailed on page four of the Star Fellows Handbook. If you google "EPA STAR Fellows Handbook" you'll see the pdf of the handbook at a scgcorp.com webpage. The introduction to the handbook says it was designed, in part, to be "a useful informational document for the general public to better understand the purpose and processes related to EPA’s STAR Graduate Fellowship Program", so I encourage you to share it with future applicants to the STAR Fellowship.
My hypothesis on the few waiting to hear is that they are unofficial alternates. There's the possibility that some people "recommended for funding" are not funded, due to not meeting requirements (for instance for use of live animals). It's easier to keep an alternate list, than it is to call someone who was declined for funding and offer them funding. Even if 98.7% of the applicants recommended are funded, that still leaves 2 slots open (assuming 150 slots total).
If you want, I'll post again when I receive the "award package".
Edit (twice) to fix weird formatting.