Gore-Tex is nothing but a semi permeable membrane, housed in a two sided "bootie" for protection. It can't stretch; doing so opens the pores at the very least and generally tears it, rendering it useless. In a static environment it works great, flexible boots, not so much. A water saturated leather outer that flexes at the toe box/forefoot junction, will create an area where that flexing action is trying to force water thru the membrane via pressure. The inner liner can also stretch depending on how the inner parts line up with your foot and the outer boot, eventually tearing the liner or opening the pores enough to allow water thru.
People mention leather treatment is needed, fact is, Gore-tex is a hydrophobic membrane by itself, it needs no treatment. Treating the leather simply keeps water away from the Gore-Tex, defeating the purpose of having it in the first place.