I've actually got exactly the same problem. I think I must have the wrong hinges but I'm a bit lost on this myself. I think the difference in the hinges relates to the bonnet opening - on Series III/IV/V cars the bonnet opens significantly wider than on Series I/II. It would make sense then that Series I/II have different hinges to III/IV/V. The flaw in my theory though is that Series III uses the same grille as I/II - if the late hinges are incompatible with the early grille, then how did they do the Series III?
For the time being I've removed the top bar from my grille which allows the bonnet to shut without breaking the grille, but I hope this is only temporary.
I've heard of other people having the same problem too, but unfortunately nobody I've spoken to ever seems to have a solution.