In court, a party asserting that a patent is invalid must prove invalidity by "clear and convincing evidence," which is the highest standard of proof in U.S. civil law (that is, non-criminal law).
In contrast, suppose that the USPTO decides that a "substantial new question of patentability" exists and therefore initiates a reexamination proceeding. In that situation, the patent examiner need only show invalidity by "a preponderance of the evidence," which is colloquially summarized as 50.000001%, just enough to tip the balance of probability. It's also commonly phrased as "more likely than not."
(EDIT: Strictly speaking, the burden of proof applies only to facts, not to the ultimate conclusion. Here, the facts --- namely what the Hillis and Nomura prior-art references say --- are are essentially beyond dispute, although I suppose conceivably Apple might find some technical grounds to allege, as a matter of fact, that at the time in question, persons of ordinary skill supposedly would not have understood those references to mean A or B or C.)
Perhaps more importantly, in the court case, a non-expert judge and jury had to assess the prior art. In the USPTO reexamination proceeding, three experienced patent examiners did the assessment.
Consider timelines, too. Even with all of the oddities in the jury results, the degree of Hogan's specific involvement in swaying the jury only came light after his own public interviews.
a) Samsung did present the evidence that the patent office relied on to invalidate but it was rejected by the jury
b) Samsung wasn't allowed to present it for some reason c) Samsung didn't try to present itOption a) or b) would provide yet another indication of a miscarriage of justice in the trial. Option c) would be be an indictment of Samsung's lawyers who seem to have performed quite poorly in many respects.