I think it's the stack size after posting blinds.

For the nash chart I use my stack BEFORE I post the blind.  I am pretty sure that is the correct way to do it. 
So if blinds are 50-100 and I have 1200, my opponent has 1800, and then I post my bb of 100, I'm still at 1200 effective stacks.
It's the most amount of chips either player can win in the hand.  So basically just pretend you go all in preflop, how big is the pot?  Divide that by two and that's your effective stack count.  Divide it by the bb and you have your effective bbs.
Hope that helps.

Oh, sorry for misleading information. I though that I read somewhere on 2+2 that it's after the blinds but now I see I'm wrong.
Lol, I've been always using it after the blinds but it's better to learn it now than never. :-D

Yea, and it only really matters much when you get into the end game.  Doesn't mean much if you're 59 or 60bbs deep early on ;)

Your not the only one rumrum,
I started off using S.A.G.E for end game and that uses the premisis of effective stacks AFTER the blinds has been posted so I just pressumed this was the same for nash. Although I do actually tighten the range in most cases so it probably hasn't effected me that much.
Great vid though, first time I've seen one that homes in on a specific area of the game.  I found it very useful :)
 
What was the HH program used in it? Never seen it before.

Something a 2p2 buddy of mine made for me to use (I use it for students, it outputs in a very nice HTML format).
He's currently fine tuning that and a few other applications for free use on this site.  That's why we have the "tools" section and why there is nothing in there yet.