This is, in many ways, similar to the issue with e-voting machines.
A few years back, in a high profile series of lawsuits, a lawyer representing some folks accused of drunk driving asked the manufacturer of a breathalyzer testing machine for access to the product's source code, so experts could review it to make sure it functioned properly. The company refused, citing trade secrets. However, a judge noted that this went against the defendants' rights to a fair trial, and said that the breathalyzer evidence had to be thrown out. Slashdot points us to the news that an appeals court has upheld the ruling noting that due process outweighs the company's trade secrets. While I have no problem with prosecuting drunk drivers, I do agree that the evidence should be solid -- and not allowing the source code to be examined is a problem.