The group Save Ellis Island who partners with the National Park Service to preserve and restore buildings on Ellis Island has run out of money and could soon be closing. After reading the article linked below it seems like it's a combination of a bad economy, and also infighting between SEI, NPS, New Jersey and New York. In the past New Jersey, who won sovereignty over the island through a Supreme Court decision in 1998, has withdrawn all funding for 2011 after having funded $650,000 in prior years. New York has not contributed to the effort.
Please note that Save Ellis Island is not associated with the Statue of Liberty or the Ellis Island Foundation.
Read a full New York Times article here.