Here are the updated charts from the issue.

The changes from this branch and shown in maroon (top panel) and dark green (bottom). During the dead-band operations, the terminal damper is at its minimum, and the flow rate is at the minimum primary flow rate minus the leakage (about 30% lower). Similarly, during cooling operation, the terminal damper opens all the way to 100%, and the air flow leaving the terminal is at the maximum minus the leakage (about 30% lower).

The TU leakage fractions are 0.05 and 0.07. The TU max flow is 0.35 m3/s (the no leakage case). So air entering the TU (or just after the TU entrance before the damper) should be 0.35 * (1 - 0.05) = 0.3325 m3/s. SPACE1-1 In Node is the node entering the zone so any downstream leakage would be happening within the TU or near the TU outlet node. 0.3325 * (1 - 0.07) = 0.3092 m3/s. So why does your figure show 0.25 m3/s? Questions: 1) where is this leakage going? 2) what is the magnitude of the leakage components (upstream and downstream output reports)? 3) What is the supply air flow rate leaving the air loop? 4) Which should equal the sum of the TU entering air flow rates? 5) What is the impact of leakage on zone air temperature if these TU dampers are at 100%.

ZoneHVAC:AirDistributionUnit,
  SPACE1-1 ATU,            !- Name
  SPACE1-1 In Node,        !- Air Distribution Unit Outlet Node Name
  AirTerminal:SingleDuct:VAV:Reheat,  !- Air Terminal Object Type
  SPACE1-1 VAV Reheat,     !- Air Terminal Name
  0.05,                    !- Nominal Upstream Leakage Fraction
  0.07;                    !- Constant Downstream Leakage Fraction

N1 , \field Nominal Upstream Leakage Fraction
   \note fraction at system design Flow; leakage Flow constant, leakage fraction
   \note varies with variable system Flow Rate.
   \type real
   \minimum 0
   \maximum 0.3
   \default 0
N2 , \field Constant Downstream Leakage Fraction
   \type real
   \minimum 0
   \maximum 0.3
   \default 0

This is what I see in the eio file:

Zone Sizing Information, SPACE1-1, Cooling, 2638.87262, 3430.53441, 0.22196, 0.28855
Component Sizing Information, AirTerminal:SingleDuct:VAV:Reheat, SPACE1-1 VAV REHEAT, Design Size Maximum Air Flow Rate [m3/s], 0.28855

ZoneHVAC:AirDistributionUnit,
  SPACE1-1 ATU,            !- Name
  SPACE1-1 In Node,        !- Air Distribution Unit Outlet Node Name
  AirTerminal:SingleDuct:VAV:Reheat,  !- Air Terminal Object Type
  SPACE1-1 VAV Reheat,     !- Air Terminal Name
  0.05,                    !- Nominal Upstream Leakage Fraction
  0.07;                    !- Constant Downstream Leakage Fraction

@rraustad - Are you looking at the correct file? The defect file is setup as follows, there are no upstream leakage define in the model.

  ZoneHVAC:AirDistributionUnit,
    SPACE1-1 ATU,            !- Name
    SPACE1-1 In Node,        !- Air Distribution Unit Outlet Node Name
    AirTerminal:SingleDuct:VAV:Reheat,  !- Air Terminal Object Type
    SPACE1-1 VAV Reheat,     !- Air Terminal Name
    0.0,                    !- Nominal Upstream Leakage Fraction
    0.29;                    !- Constant Downstream Leakage Fraction

Oh, I saw 5ZoneWarmest and looked at and ran the example file, in Chicago. 0.35 * (1-0.29) = 0.2485. Now the numbers make sense but I still would like to see the leakage plots just to make sure they do what we expect. I see what you did and why but we should make sure everything works correctly. I would think the SA flow rate equals the sum of TU entering air flow rate and suspect that would match because the simulation would go to max iterations if it didn't so you probably don't need to look at that. Does the leakage go to the zone (a cooling effect)? The plenum? Is it the correct flow rate?

Zone Sizing Information, SPACE1-1, Cooling, 2634.04754, 3424.26181, 0.26406, 0.34328
Component Sizing Information, AirTerminal:SingleDuct:VAV:Reheat, SPACE1-1 VAV REHEAT, Design Size Maximum Air Flow Rate [m3/s], 0.34328

Docs don't say where the leakage goes:

Here it is in the Eng Ref. Says the leakage goes to the plenum, but this is a downstream leak so where does that air go?

Again from the Eng Ref, the leakage flows vanish. I suspect both upstream and downstream are added to the plenum but this suggests that at least the downstream leakage is not accounted for (because elsewhere it says upstream leakage goes to the plenum), which I think should either go to the zone of the plenum (if it exists). The last line says these leakage flows are added to the plenum.

@mitchute I've looked at this from all angles. This change looks correct.