Let me throw this into the mix...
Do you boil according to time, or to volume? For instance, on my system my evaporation rate is 1.5 gallons per hour, but I can only achieve that under "perfect" conditions. If there is wind, the boil time increases because the heat gets blown out from under the kettle from time to time, preventing a good consistent rolling boil, which in turn affects the evaporation rate. So, rather than watch the clock, I watch the volume marks on my boil kettle.
Last weekend, it was windy and rainy. My brew area is protected from rain, but not quite protected from wind swirling around. My boil took nearly 2 hours; there were several times when the wind reduced the boil to a simmer for a little bit, but I kept going until I had reached the final volume of wort I was looking for. In addition, I check the gravity during the boil with a hydrometer and keep going until I hit the gravity I want. By watching the rate of evaporation, I can time my hops additions accordingly.
Things like pH and malt crush are certainly important, but I do believe that before you can look at those, your process must be sound.