My les paul copy is all tuned in correctly, correctly intonated but for some reason if I play F, Am, A, it sounds out of tune. Picking each string slowly it seems the b and g strings are causing the trouble.

guitar.wma - 0.26MB

Here's an example of am and f,

I just don't know what else it can be?
put some new strings on and check you intonation, you have to redo it every now and then.
A hero of war, Yeah that's what I'll be

It almost certainly sounds like an intonation problem.

Even though it intonates perfectly at the 12th fret and open, not every fret will be right on the mark.
I have had new strings on 3 days ago, and I took it to a tech who intonated it for me, and I've rechecked it this morning and it's still like this. Bought it in sept. So definatly intonation problem?
There's a few things you can do.

Check that you're not pressing down on the fret too hard or bending it slightly, as this can make the note go sharper because of the extra tension.

Play the fretted notes and check them with the tuner, if the tuner says they're out of tune, but in tune at the 12th fret of the same string, then it's an isolated intonation - pretty common on lower end guitars.
I've fiddled about with it, still can't do it, moved the saddle up and down, still the same out of tuneness. Am i really stuck with it like this
I've sat and fiddled more still can't. I took it to a repairer who turned the bridge around because of this problem but I've still got it. It's def green on all 12th frets and open. So what else could it be?
Possible warped neck...look down the neck from the body of the guitar. It should be nice and straight. Did your guitar tech check this for you?