Always visualize your results with other means, in this case align against the genome. Once you look at your data with IGV the answers will be more forthcoming.
Are you getting so few results because the data is perfect, everything comes out the same across all samples? (this is usually rare)
Then perhaps your replicate variability is such that the intra-replicate consistency is comparable to the variation across conditions, in which case you are finding these few results because the evidence for variation across conditions is just not there.
Finally, I will say that I only had such a problem a few times, when studying brain samples from an excellent scientist whose data always turns out to be nearly perfect, text-book like consistency across replicates.