Cedar Shingle Roof Moisture ingress or mould?

So they are fixed into the plywood frame with spax caped screws, but its an opening made specifically so its not allowing air to flow in as its tightly clamped and sealed with silicone etc. That said, we have a part of the front facade that is not yet insulated, see the screen grab.

I have also included a detail of the polycarbonate Multiwall/windows. I hope thats clear?
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OK but how are the windows sealed? What are the others made of - they just look like thin perspex screwed to the frame over a seal, any hybrid windows like that will be prone to water and air leakage etc, suspect that will be the cause of your high humidity.
 
general comments
with ply it can be very difficult to find the entry because off crisscross layers and often manufacture gaps between the butted up veneers but in general it will usually be just above the leak to at the top edge off the sheet
have you though about the overhang on the top off the roof catching rain with wind in the wrong direction this will off course depend on the construction permitting this
 
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That's saying condensation mould to me, and a design issue not water penetration.

Ply is highly susceptible to mould with very little humidity tolerance, and multi foil is a poor performer with convected and conducted heat when placed in a composite structure - many are still unconvinced that it works as stated by the manufacturers as it has been tested in a different way to make it appear to perform.
 
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