Originally Posted by: gplayer33I am studying music theory to become a better guitar player.[/quote]
Good for you! :)
[QUOTE=gplayer33]
Anyways I understand the minor pentatonic scale to be Root, b3, 4, 5, b7.

That is true. But it is sometimes better to think of the 3rd, and 7th to be minor instead of flatted. This is because the scale intervals could land on a flat or a natural note depending upon the scale you are studying. And that could potentially case confusion.

And you have it right. E minor pentatonic:

E - 1st
G - minor 3rd
A - 4th
B - 5th
D - minor 7th

The note G-flat is only a distance of 2 frets from E, this makes is a 2nd, not a minor third. I think you are confusing the idea of a flat with a minor interval.

Look here at my tutorials that cover the pentatonic scale in theory and practice:

http://www.guitartricks.com/tutorial.php?input=296
http://www.guitartricks.com/tutorial.php?input=722
http://www.guitartricks.com/tutorial.php?input=185

Best of success!