I saw an interview on TV(EWTN), and she explained what she was going through spiritually. She still had faith in Christ. However, she did not feel his presence anymore. Yet she still dedicated everything she did to Jesus. It was a very, very painful time for her. She never did lose her faith. Mother Theresa had a deep love for our Lord. How can you say that you love someone if you don't have any faith in them? She expressed her love of Christ all the time.
I’ll refer you to RnMomof7’s post here...
http://www.freerepublic.com/focus/religion/2578704/posts?page=7565#7565