If it is accurate, Obama has 53.55% and Clinton has 46.44%. So the proportional system is actually working, despite all the quirks in individual states. Obama's roughly 5-point vote lead has translated into just over a 7-point lead in delegates. That's an advantage ratio of 1.08, which is fairly typical of a moderate-magnitude PR system. Clinton's advantage ratio is slightly smaller (1.04).
In California, where Clinton won the vote 52%-42.3%, she won the delegates, 54.9% to 45.1%. So, Obama had a very slightly bigger boost (ratio of 1.067 compared to Clinton's 1.055). Not much, but consistent with expectations we had due to all the even-magnitude districts.
When I have a chance to look at other states, if anything anomalous comes out, you can be sure I will say so!