You do not have to get rid of them. The first spike is depending on the initial moisture of your construction. In the first year/ years the initial moisture is being redistributed, your construction tries to come to its equilibrium.
I see, but since the construction is already assumed to be in equilibrium, tho it is build 500 years ago, we figure that the spikes will be misleading. If we use the last years in the calculation we will get rid of them but then we won't be able to se the inital changes when we apply our modified climate. We spent alot of time trying to adjust the inital moisture conditions in the layers but perhaps it is not possible to change it that way.