Hmm 2nd post today concerning problems with Spanish bureaucracy - is the heat getting to them as well (the Spanish are talking about the heatwave, not usually a topic of conversation)
I have many years experience of getting NIEs for clients (when we were selling houses) and NEVER had a problem - getting an NIE means that you will be paying some form of tax in Spain which is surely good news for them!
Another (maybe a bit cynical) suggestion I have seen is that perhaps they now only want to deal with persons using gestorias or the like (I expect they are suffering with the crisis, funny how every abogado down here is suddenly a tax expert given they are not busy with house completions).