I know that Mother Angelica did question the supposed reading of the whole Third Secret of Fatima back around 2000 and even had the Traditional Latin Mass showing on EWTN for a time (I even caught a glimpse perhaps of when that happened one time.) Not too long afterward she was pretty much ousted by the Novus Ordo establishment and already had a struggle with her health and age.

Requiem aeternam dona ei, Domine, et lux perpetua luceat ei. Requiescat in pace. Fidelium animae per misericordiam Dei requiescant in pace. Amen.

Around 1995, I set up my mother's TV for getting EWTN by Dish antenna.  She had no interest in the other stations, but got the service just to get Mother Angelica's programming.  That served her well for about a year or two, and then the questionable material crept it, or at least my mother became suspicious of what had been there all along, I'm not sure.  But I can't look it up on Google so I guess I'll never know for sure.

When the TLM was broadcast, I looked into the oddities I saw, and I soon discovered that it was actually a hybrid liturgy.  They were using a mix of Latin Novus Ordo parts along with Traditional prayers.  Also, they arranged the sanctuary so as to APPEAR that it was ad orientem when the rood screen behind the altar separated it from the actual congregation (the "cloister") which was located there ostensibly "behind the altar," effectively making the altar oriented to face the people (the "people" being the nuns in the cloister area)!  In most convents I have visited, the cloister is located to the SIDE in a transcept, not behind the altar.  The studio audience was set up where the choir would be in a Protestant church, which gave the impression on TV that it was not mass facing the people (but it really was).  So the larger floor area was granted to the space truly behind the altar, effectively appearing to be in front of the altar (celebrant facing the cloister), with all the TV cameras there, facing the same direction as the celebrant like they would if filming a TLM.  And the smaller floor area was allocated to the space truly in front of the altar for mass facing the people (the cloister) without any TV cameras present.  

They might have tried to conceal their illusion mostly from Mother Angelica, and could well have given her all manner of technical reasons why they had to set things up that way, just to avoid her resistance to their schemes.

I saw the original broadcast when she said that regarding those people who don't think the revealed "third secret" was the whole thing, "I'm one of those, because I don't think that's all there is."  (I might have a few word imprecise - but that was her take on it.)  I was impressed with her courage, but she was always one for spunk.

After that, she was quickly phased out, and the changes and updating accelerated conspicuously.  Looking back, it seems she may have known that her time was up, and she put in her last "harraugh" for the real Third Secret, bless her heart.

 
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http://www.breitbart.com/big-government/2016/03/28/mother-angelica-plainspoken-nun-founder-of-global-cable-network-dies-on-easter-sunday/

As outspoken as she was and as conservative, too, Mother Angelica was not afraid to cross swords, even with powerful Bishops. When famously liberal Cardinal Roger Mahoney issued a letter she thought “watered down the Real Presence” of Christ in the Eucharistic bread, she rebutted his letter point by point on TV and refused to back down when he threatened her with losing her religious community and her cable network. She was quoted as saying, “I’ll blow the damn thing up before you get your hands on it.”

  God bless her, she was a real fireball.