So, while playing through the game, I noticed that the USA flag is quite different in the game opposed to the one irl. I just thought it was some sort of a new flag made after the divergence, but when I read the news earlier today, I saw that same flag on a picture from the voting place in Dixville Notch, New Hampshire.

So my questions are, what's this flag representing irl, and how did it become the official flag of USA in FO? (Or rather, the flag of the enclave i guess)

Here's a link to the news article btw, it's in norwegian though, but you've probably read it all before anyway.
http://www.nrk.no/nyheter/utenriks/valg_usa/1.6293552

According Fallout wiki, which contains source material that may or may not be canon but came from people who developed the game, the flag was adopted when the US reformed itself sometime in the past. It created "Commonwealths" a mid-level government entity which combined various states so as to more effectivly control them. There were 13 such Commonwealths, a number chosen for obvious reasons. The outer ring of stars represents this. The center star represents the unity of the nation.

zomg! The enclave are forming in new hampshire!

So it begins...

It's very similar to the Cowpens Flag.
(See Wiki: http://en.wikipedia.org/wiki/Cowpens_flag )

According to the fallout bible i just downloaded from GoG they just wanted the flag to look different and were going to have something about 13 "superstates" but never got around to it so it really doesn't mean anything.

The closest thing to a state in fallout is the New California Republic and that has about 3 cities in it

It wasn't fully developed by the devs of the original Fallout, but the developers of Van Buren (the canceled Fallout 3 by Black Isle) came up with a detailed division of the country into 13 commonwealths:

http://fallout.wikia.com/wiki/United_States

Okay, well the wiki says 14 stars... but the one in FO3 has 13 stars total. Trust me, I have a screenshot.

Yes, the FO3 one only has 13 stars, probably by mistake (the Fallout 1 also appears not to be entirely correct either). Leonard Boyarsky's original intent was for it to symbolize 13 super-states (later called commonwealths), with 13 stars in the middle.