I doubt that there is anything else going on. These things are highly publicized now and we would have heard something from the government. Someone would certainly want to claim political credit.
For example, the special registration program was announced by the White House, by the Attorney General and by the INS. The new rules were published by INS around Sept 11 and there were a lot of news stories about it, both on TV and in the papers.
I do not believe that what you really saw on FOX was people holding green cards being fingerprinted in the airports. The way these news stories are put together is often rather loose: they talk about one thing and show footage of another.
This is particularly true since news reporters have no idea about US immigration laws and do not understand the technical meaning of various legal terms (like immigrant, non-immigrant, visitor, etc).
For example (and this is what most likely happened), they could have shown an immigration control line in an airport. Obviously, every arriving from abroad passanger has to stand in such a line, PR or not, subject to the special registration or not. PRs would naturally be holding their plastic green cards while waiting in such a line.
Some people, namely the non-immigrants who are covered by the new special immigration rules and also have to stand in this line, would be fingerprinted when passing the immigration inspection. Others, like PR holders and the other non-immigrants, would not.
Or they could have even shown a line at some INS office where people bring their PR approval notices for passport stamping and, naturally, get fingerprinted.
The only news stories regarding fingerprinting that I found in the Fox news archive, concern the new special registration program:
http://www.foxnews.com/story/0,2933,54789,00.html