Possibly because the dates of the tournaments are different this year. So the 'drop date' has moved. Having said that, Monte Carlo is not listed at all under Djokovic's points breakdown. The ATP never explains things properly...
I just realize that Roma was earlier last year, Nadal lost those points this week.
Nothing is wrong, he will get those points back in two weeks if he wins again.
About Djokovic, I know they don't have to go to Monte Carlo that is why he didn't get a penalty. I understand that but, that means if Nadal doesn't go to Monte Carlo next year he will keep 1000 points and he will never lose them?
I am really confused about this.