Yes, it is a bit of a mystery and not easy to understand. Every component in the fuel system affects the flow and pressure slightly. Every hose, every fitting, filter, check valve, etc. The placement of such things all has influence, in most cases very slight. The metering valve has a huge effect on this however. Look at the typical Enderle cube for example...the fuel changes direction many times (90 degree corners in most cases). There's a pressure drop at each point in the system and this causes the pressure to differ depending on where you measure it. The fuel flowing through the system has momentum/inertia and when it hits a corner, it's higher on one side of that point and lower on the other. After several such places, it can change quite a bit.
If you put a pressure sensor before and another after the barrel valve, you'll see a difference, even at WOT. Sometimes as much as 20 PSI or so. Pressure backs up against things, is relieved in certain places (check valves and passages in the BV that lead to check valves), and the spring loaded poppets in the check valves cause a strange situation with pressure at that point and upstream.
Pressure reported in the calculator isn't always correct, but it should be fairly close for a given metering valve style. Since putting a box in the calculator for pressure correction would just confuse people and cause endless questions and head scratching, I chose to just use correction factors for each that are typical for what we see flowing systems. It's a ballpark idea to help people choose nozzles.
When we find big discrepancies in pressure, there's generally something causing it that's easy to identify. For example, running a blank pill in an Enderle barrel valve and running a drop-in style pill in a "main" check valve after the pump can cause actual system pressure at the nozzle to be quite a bit different than what we'd calculate. The system still works great...no problems with doing that and the tuneup is basically the same. But pressure is affected.
Spud
