My doubts began with the reinstatement arrangement. I wasn't so much bothered by the disfellowshipping arrangement at the time. However, the process to come back into "the truth" seemed excessively punitive and a form of cruel and unusual punishment. For years on end i would see different ones sitting in the back in assigned seats (Yes, that's right. In the country I live in they actually are assigned where to sit!) being treated as if they were quarantined. My heart went out to them as they were shunned every meeting, yet they continued to come for more punishment week after week, month after month. I checked the bible and ran into JWfacts and realized there was no biblical support for such a cruel arrangement.
The second thing that got the ball rolling was the earthquakes and Tsunamis that killed hundreds of thousands over the last 11 years. To me, God is the only one who knew they would happen. He has the power to show his love/mercy and warn people or stop the earthquake all together. Yet he didn't intervene as children and babies were crushed or drowned.
I remember clearly the tsunami of 2004 (as I was living very close to the nations that were devastated by it.) At first I was actually excited. This is a clear sign that we are living at the end of the last days! Then as I saw the level of suffering and death, I just got angrier and angrier that our loving god did nothing to help. I could no longer fault people for being atheist or agnostic and that really affected my ministry. After that, the small stream of doubts steadily grew into a raging roaring river that swept away everything that I had held to be true.