The controversy has apparently been settled. The explanation is both deflating and clarifying. In essence, Umpire Doctrove was certain that Strauss had completed the Hughes catch, while in the case of Bopara, neither Umpire was sure that the catch had been completed. The Australian contention is that had Hughes's catch been referred, a verdict in Hughes's favor would have been returned, as video replays were inconclusive.
Video replays are never going to provide enough information, because they involve the projection of a 3D video on a 2D plane. As a result, even with the benefit of a perspective projection, at those very short distances (such as between the ball when it first hit the hand and the ball when it then lodged in the fingers), it is impossible to get any perception of depth. The result is that the ball appears to drop to the ground, when in fact, it is probably falling away from the screen.
This is a well understood phenomenon. What is often misunderstood is the consequence of this lack of information. Even in cases where a TV Umpire determines that the catch that he sees on the screen has been completed, he is still doing so based on bad, incomplete information. Hence, even in cases where the umpire determines that the batsman is Out, the decision is no better than the decision from the on-field umpire.
So both the Out and the NotOut decisions, made by the TV Umpire are based on dubious evidence (except in cases where the catch is shin high or knee high!). The obvious problem lies not in the technology, but in the total break down of trust between the batsman and the fielders. No batsman can afford to trust the word of the fielding side (certainly not in a major Test Match contest). Even if a batsman is inclined to take the word of a fielder, the pressure from his own side and supporters will be too great, for they will point to an instance where an opposition batsman didn't act in the a similarly gentlemanly way and went on to make big runs.
As in the case of Hughes and Bopara, the "correct" decision, such as it is, depends on whether or not the onfield umpire can be certain that a catch is clean or otherwise. The minute an on-field umpire refers it upstairs, controversy is inevitable.
There are solutions to this problem. Some are well known and have been suggested for a long time. The most obvious one is to reinstate the old law, which stated that in order for a catch to be clean, no part of the hand below the wrist (i.e. the palm the back of the hand or the fingers), should be in contact with the ground when the ball reaches the hand. This change will favor the batsman. However, there are any number of rule changes which could redress the balance - reinstating the backfoot no-ball rule being the most obvious one. Rarely has there been a law which promises so much good, but has been set aside, mainly due to inertia.
A more radical solution to this problem would be to give the close in fielders place mats - astroturf mats. The fielders will definitely complain, but if the mats are sized correctly to accomodate a dive by the catcher, this would ensure that the fielder would always dive on the mat, thereby ensuring that background for the catch is a flat surface, and not grass. But this is a complicated solution and as such is quite impractical (even though impractical rules abound in the modern game - one only has to look at the new chucking law)
As things stand now, they are ripe for Ricky Ponting and his ilk. Like his predecessor Steve Waugh, im fairly certain that to the end of his playing days Ponting will continue to insist until he's blue in the face, that his Australians play 'hard but fair'. Then, once he has retired, he will, like his predecessor, admit that his Australians "got away with murder". Whats more, he will probably be convinced that he held both positions absolutely sincerely!
Given the impossibility of implementing the law without any trust amongst opposing players, Ponting's prospective conviction is a self-fullfilling prophecy.