So I have a couple theories on this. None of them might be true, and they all might be true, but they're just thoughts:
1) Experience. Knowing God myself certainly provides me with a significant amount more confidence in what I believe than it would if it were all empty doctrine with nothing real to back it up with. However, I don't believe all "Christians" can claim this.
2) Social setting/upbringing. Living in tightknit Christian communities, being brought up with a very explicit definition of truth. Many never challenge the status-quo and think about stuff for themselves, instead just accepting everything pass on to them at face value. Even if what is being passed on is true and just and all that, over time this causes the message to become mixed with the influences of everyone passing it on. It can seriously distort the original.
3) Multiple viewpoints? I'm not sure which instances you're specifically referring to, but I know that sometimes if you're trying to get people to work together, you give one person one clue and someone else another, making it far easier to solve the question if they both put their clues together (specifically referring to your Holy Spirit question there). However, if two Christians have conflicting viewpoints on an issue, I'd imagine it's either because their own influences differ. Theres multiple branches of the church who still don't agree on everything (Catholics being the most out there, but there are still some differences between Anglicans, Baptists, etc.), and some areas are just plain grey areas which don't have black and white answers.
4) We're only human ourselves. This isn't an entire answer, but how can I claim to fully understand a God beyond time? My understanding is limited at best, and so there will be times when we will conflict because one or all of us aren't accurate in our understanding. However, I'm more than prepared to simply try and tackle what seems illogical or stuff I just don't understand, and attempt to gain an understanding of it. We generally sort stuff into two baskets: stuff I have gained understanding of (i.e. I'm confident over the answer to this), and stuff I'm still trying to understand (i.e. I'm confident there is an answer to this, but I don't know what it is yet). Some people don't even like having that second basket at all and try to make quick answers that often don't make sense.