Demosthenes, it is not that confusing if you read carefully. In the first quote they are refering to genes. That is, defined stretches of DNA that has been annotated to carry coding information. 99% are annotated to have the same function, but may vary slightly in the sequence.
In the second quote they compared whole DNA stretches (I admit, I got the issue lying around here somewhere but did not actually read it...). So in the second quote they basically say that we do not only have the same genes, but even the sequence of them is very similar (with exceptions).