When I was first having problems with "the truth" it was because I started to believe in evolution. I first tried to mesh the two but it didn't work. Here is why I believe evolution is incompatible with the Bible (or at least my understanding of the Bible):
If evolution happened (and of course it did ), man would not have "started" with two humans. There would have many. This causes a major problem with the whole "original sin" concept because it requires that only two humans existed, they both sinned, hence sin was passed to all offspring. If other humans had existed at this time, sin would have only spread to the decendents of that human pair.
Second, humans did not evolve from chimps. Chimps and humans have a common ancestor. Humans, according to the current "guess" evolved from neandertals (which are now extinct). Neandertals would have had some reasoning ability, probably some form of morality, etc. Why would God not test the neandertals? Why did he wait until they evolved into humans?
I could not find a logical way to mesh evolution and the bible, so I ended up tossing out the bible as God-inspired. I also no longer believe in God and consider myself ahteist.