I was thinking about Skyfall and the way we discuss why Bond has lost a part of who he is and how he regains it, and the answer actually seems quite obvious:
From the moment Patrice's depleted uranium shell enters OO7's shoulder, he is being poisoned by the shrapnel.
From the moment he removes it, he steadily returns to form.
All of Bond's woes can be put down to this shrapnel.
Depleted uranium (DU) is not just radioactive, more importantly it is chemically toxic
to the human body and will create a selection of physiological and neurological symptoms which neatly explain the results of his tests.
(For more info on these effects, check out http://en.wikipedia.org/wiki/Depleted_uranium#Chemical_toxicity
In the film, we can see that by the time Bond collapses during the tests, and is bemused by his inability to hit the target with his Walther, he knows something is wrong inside his body. He rejects the idea that he has "lost a step" and takes a knife to his own body to remove what he suspects might be causing the problems, with the added benefit of identifying Patrice more quickly... something he could have done by spending a few hours sat at the Identograph. :)
So just as Bond is at his lowest ebb before he removes the shrapnel, we can see by his swim in the hotel pool in Shanghai that he is almost match-fit again.
This makes me think that during the scotch marksmanship scene, Bond is in complete control of his actions, from before he even set foot on the island. Severine has been a means to an end, and he considers her expendable (she has after all been complicit in at least one of Patrice's murders and is a villain).
As he shakily points the musket at the glass atop her head, he knows he can make the shot, but he misses on purpose so that he can spring into action moments later and capture his prize.