i had this exact problem and done a ton of reading from all different sources and made my own little guide for everthing to do with chord progressions (since i have never found a definitive guide for the n00b).
ok, according to my guide,
the iii is minor because:
the chord (the third triad in this case) is E,G,B.
The distance determines whether something is minor, major, augmented or diminished.
in this case, the G is exactly 3 keys from E (do not take the scales notes into account, you include ALL keys, black and white). it goes E, F, Gb, G. therefore the third is minor.
if the fifth (the third key of the chord, in this case B) is exactly 7 from the root key (E) then that is a perfect fifth, which means the triad will be whatever the third was (we calculated minor since G is 3 keys away from E). in this case the fifth is indeed perfect, as B lies 7 keys or half-steps (every key is a half-step to the key immediately next to it) away from E.
In the first example (I), the triad is major (indicated by uppercase I). this is because the chord is C,E,G. E in this case is not 3 (which is minor) but 4 keys or half-steps away from C.
so for the second key, 3 half-steps from the root note indicates a minor third (second key) and 4 indicates a major third.
if the fifth (the third key of the chord) is exactly seven keys (dont take into account the scale you are in) from the root note, that chord is perfect, and it is either minor or major, whatever the second key is.
This is not in your example, but sometimes there is a little circle next to the numeral, or a plus sign.
if the fifth (the third key) is 6 half-steps ahead of the root, it is a diminished triad (regardless of what the third [second key] is). in this case you write the numeral in lower-case and add a little circle next to it. if the fifth is 8 half-steps (instead of a perfect 7) from the root, it is augmented, and the corresponding numeral is written in uppercase and a little plus sign is added to the right of the numeral.
as you can see, if a triad is minor in a major scale it does not matter....
man i hope some of that made sense... good luck!