I also have this problem if I don't use my mom's recipe! I misplaced it and then after she died, found it inside a notebook in her kitchen. This one never runs for me, I think its the flour. This was my grandmother's recipe as well. Being from Texas, we love our pecan pie and we don't like it runny! Here it is:
1 cup sugar
1/4 cup flour
1 cup Karo Dark syrup
1, 5 0z. can evap. milk (roughly 1/4 cup of evap milk)
3 eggs beaten lightly
1 cup pecans
Mix the flour and sugar together, then add the syrup, evap. milk and beaten eggs. Mix well, with a wooden spoon. Add the pecans, pour into a pie shell and bake at 350 for 45-60 minutes. If it begins to look too brown on the top, place some foil loosely on the top but keep it baking. Undercooking is often the culprit of runny pie!
I also make sure I make it either the night before or at least 6 hours before I serve it.