Here is a link to the paper referred to in the 99% article:
http://137.122.151.29/...es/pdf-includes/Chimp_Human_DNA.pdf
The paper states that there is a 1.4% difference due to base substititions but an additional 3.4% due to indels. These are much rarer events (1000 indels:10,000 substitutions in the sample) but because they can be very large (up to 4,000 bp) a single event can make a big difference in sequence.