What, if anything, has caused you to question your faith?
I would first like to make clear that I am not certain Christianity is true, nor am I certain that God exists or anything like that. I have come to believe in certain truths such as these because they seem most probable, not because they are beyond all possible doubt to me. So, for me, it is not a question of being sure of Christianity and occasionally having isolated issues or arguments that seem to undermine that, but rather this concerns the balance of probability and how strong certain factors may be. For example, I normally grant that arguments from suffering have some strength as evidence against the existence of God, but that it is not sufficient to make theism improbable.
Granted this, I believe that there are certain factors which may count against Christianity. I do not ignore these issues in order to hold onto my faith, nor do I believe even more avidly *because* of them- I have heard this response before by those defending Christianity (or some other worldview), and I see it as entirely unreasonable. It is merely that I do not think that the arguments are strong enough to make Christianity improbable. One example would be the enormous extent of suffering in the world, and sometimes this has more force to me as an argument against Christianity than at other times. Natural evil (for example, earthquakes and floods) is particularly difficult to explain. Another example would be related to severely diminished cognitive capacities among particular individuals, disorders that may severely limit their response in relationships, both among humans and towards God. Whether this has any force depends on which particular type of Christianity one holds to. For someone who believes in universal salvation, it may not pose much of a problem since they would probably hold that God would, to the extent that cognitive diminution restricts an individual’s capacity to form and act in relationships, ultimately redeem those difficulties so to allow a fully effective relationship with God and others.
So I am willing to admit that there are difficulties, and happy to try and think of some more. One important point, however, is that simply *not knowing* something given a Christian worldview does not necessarily count as evidence against that worldview. To say that I do not know why, for example, God created crocodiles does not mean that the existence of crocodiles counts against Christianity. A Christian not knowing the answer to a particular question would usually only count as evidence against Christianity if either:
a) If Christianity were true, it would be probable that the Christian would know the answer
b) An exhaustive list of possible answers is produced, each of which, if true, would undermine the truth of Christianity.
There are other instances (and feel free to get in contact if you want me to elaborate) where a Christian not knowing the answer to a question would undermine their faith, but it should be clear that not knowing an answer to a question, how to resolve a particular difficulty or how to alleviate a particular doubt does not count against Christianity unless it is demonstrated that one of the above situations holds.
I hope that helps!