The issue's apparently been resolved and Gaga is now permitted to go ahead with the concert on June 3.
A press conference with the tour promoters, the police and FPI took place earlier today by which they revealed it was not just a religious dispute, is was also about money / taxes. The concert in Jakarta alone is expected to gross over $4M but the officials wanted more money for the event as it is to be the biggest concert in Asia / the biggest ever in Indonesia.
The press conference will air later this afternoon in Indonesia.