My problem is this. I know that to create a minor chord you must flatten the third. Easy Enough.
However, I've read (and i'm led to believe) that G Minor and C Minor are impossible in open string positions (the basic open string position).

When i study the voicing of the G and C Major open chords i find the 3rd note sure enough.

G Major Chord is the notes GBGDBG (thinnest to thickest)
3
0
0
0
2
3

I then find that it (along with C) is the only open string chord with two possible third notes ie two b notes in the chord. Now by using the B string as the third in the G chord, i can see how a minor chord in this position is impossible. However by using the B note on the fifth (A) string, flatting that third creates a A#, which by rights should be g minor. What The.....?

What perplexes me even more is that by using that B note on the fifth string and raising it i can create gsus4, just like any other chord? And this is recognised as correct.

So I'm basically asking which is the 3rd note, is it the b string or the b on the fifth string and why/why not?
If it wasn't for bad luck, I wouldn't have no luck at all
the b on the b string and the a string are both the third, remember you can repeat notes in a chord. if you really wanted an open Gm you could play

3
3
0
0
1
3

or for Cm

3
1
0
1
3
x

but both of these are pretty damn tough to finger, so most people just play a bar chord
The third note is the note that comes third in the scale....therefore for a G major chord it's the note that comes third in G major which would be the B on the A string, technically the open B is a 10th because it's in the 2nd octave of the scale. However, having what amounts to a major and minor third in the same chord will sound very odd so for a G minor your options are to either flatten the B on the A string as you've already discovered and also fret the open B at the third fret to give you another 5th (awkward fingering alert!)

e|-3-
B|-3-
G|-0-
D|-0-
A|-1-
E|-3-

...or mute the A string and barre the top 3 strings at the 3rd fret to give you a minor third on the G string, like this.

e|-3-
B|-3-
G|-3-
D|-0-
A|-x-
E|-3-
Actually called Mark!

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However by using the B note on the fifth (A) string, flatting that third creates a A#, which by rights should be g minor. What The.....?

Just a pedantic thing - when you flatten B, you get B flat(Bb), not A#. Theyre the same sounding note but have totally different functions within the key of G. The 3rd of G is always going to be some kind of B.
thanks for the help
If it wasn't for bad luck, I wouldn't have no luck at all