Carlos Moya explains what happened with the Madrid courts. The problem, he says, was salt. I don't have time to translate the whole thing, just give you the gist of what he says.
http://deportes.elpais.com/deportes/...63_765218.html
Moya says during the first three editions of the tournament there had been some problems with the courts as well. Because of this, they wanted to make an extra effort to ensure there would not be any problems the first time on blue clay.
They opened the courts to the public several months before the tournament so people would come, walk on them and play on them. They also had an agreement with the Madrid federation so that local schools would come and use the courts. Moya says he himself tried the courts several times. He played with Pato Clavet and other players, and says they didn’t notice anything unusual except that the the bounce was a bit lower than on the red clay. He says Javi Martí (ranked 174) also tried the courts several times and never had any complaints. Moya played on them for the last time on 3 May before leaving for a senior tournament in Medellín (Colombia). He didn’t notice anything strange. Then, from Medellín, he spoke with some on the players already in Madrid, including Rafa, who told him the courts were unplayable. He thought maybe he was exaggerating, but there were other players telling him the same thing.
When he came back to Madrid on May 8 he went straight from the airport to the courts to see what the matter was, and he was amazed to discover that the courts had become something completely different from what he had tested. “I couldn’t believe it. It was impossible to get any traction on them and I had seldom seen a clay court in such slippery condition.”
After much wondering and trying to figure out what had happened, the team that built the courts suspected the problem was the salt. He says they use salt also at Roland Garros and many other tournaments, to preserve the humidity of the clay and give it a more uniform color. With the water and the high heat in Madrid that week, the salt “crystalized” into an unbreakeable film on top of the surface, making it very slippery. This was discovered too late, and showed that what may work in Paris doesn’t necessarily work in Madrid.
Goes on to say that the Madrid altitude, plus the lower bounce on this kind of clay, combined with the courts becoming a “skating rink”, was a "lethal combination" for the defensive players and they all thought Federer was the favorite, as it turned out.
He says it’s a pity all these unforeseen developments ended up creating a rift between Nadal and the tournament, and says it’s not to late to try to mend things. Says next year should be okay because the courts are going to stay on the entire year etc. That’s assuming the ATP allows the blue to continue.