The way I read the story at Velonation, they confused the APMU and testing and mixed the term software into the confusion. I think the UCI likes the story that confusing though.
According to WADA documentation, the UCI tells the lab which samples to test. Those tests generate a bunch of documentation. That documentation is passed to the APMU. The APMU has some software to track all of this stuff. The APMU passes suspicious values and lab documentation off to experts.
The UCI's claim is the APMU was not managed by the UCI, so it would be the lab providing the APMU service on top of their testing service. This changed in 2012. Now the sports federation is the APMU. That's a wonderful opportunity to suppress positives.
As I understand the WADA documentation, the non-suspicious test results means the APMU does not pass on the results to an expert. Why would they? Passing results to an expert generates meaningful costs. The anti-doping experts are not working for free.
No. Statistics is pretty good at establishing good-enough sample sizes such that one can be confident testing a small population as representative of the whole.
Here's where things get murky and IMHO that is intentional.
-If you are a smart doper, you higher a doctor who has figured out dosage and timing such that the athlete never tests positive. Floyd Landis states plainly that he and presumably other riders were examining their own blood to stay within some non-positive parameters.
-The UCI dicates who to test and what tests and they know which athlete codes match the athlete. Plenty of opportunities to lose some tests, not test for certain drugs as was done in the Giro, and probably many more clever ways to divert tests.
I posted some other boring details here:
http://forum.cyclingnews.com/showpost.php?p=1137882&postcount=295