I am sure there can be a couple reasons. One might be that boiling drives off CO2, CO2 in solution will drive the pH down. pH measurements are also temperature sensitive. I think most test strips are optimized for 20C (68F), hotter liquids will tend to make the pH read higher.
Also, pH of your water has little to do with the pH of the mash. The pH of the mash is controlled by the hardness of your water and the residual alkalinity in the mash. If you have water with low buffering capacity and are trying to brew something dark, this can drive the pH of the mash down, you should consider correcting with sodium or calcium carbonate.
I highly recommend the Brew Strong podcast dealing with water, John Palmer explains every aspects of brewing pH and making adjustments very well (4 shows):