I wonder if it was stored flat on battens at some time?

put a straight edge across those aeras and see if there is a slight gap under it. ie check if its shallow. also check if the surface feels different. it may not have been sanded properly during manufacture.

gzt: The second sheet has similar marks in a different location. What brand and grade is the plywood?

Yes, I think it's in all of the walls, I'll need to find out from the builder the brand/grade of the plywood. 

k1w1k1d:

 

I wonder if it was stored flat on battens at some time?

 

The top and bottom borders of some of the marks are not straight and not parallel - so storage on battens is not likely to be the cause.

The way the marks run horizontally and are evenly spaced may indicate that they were made by the machinery used in the manufacturing of the ply.

Some log-peeling and plywood-making machines use conveyor-bands that are about the same distance apart as the marks on your panels - see around 2m20s in this video.

eracode:

The way the marks run horizontally and are evenly spaced may indicate that they were made by the machinery used in the log-peeling process during manufacture of the ply.

Log-peeling and plywood-making machines use conveyor-bands that are about the same distance apart as the marks on your panels - see around 2m20s in this video.

@turtleattacks Is the wall going to be painted? If so, the marks probably aren’t going to be an issue.

eracode:

 

The way the marks run horizontally and are evenly spaced may indicate that they were made by the machinery used in the manufacturing of the ply.

 

Some log-peeling and plywood-making machines use conveyor-bands that are about the same distance apart as the marks on your panels - see around 2m20s in this video.

 

Alternatively, if the log is held against rollers while it’s being peeled, the rollers could be making the mark continuously on the veneer as it’s being peeled. Like the ‘printer-drum effect’ mentioned above. This may be more likely than the conveyor bands I suggested earlier.

Any reasons why this wasn't there when we first put it up and showed up a few weeks after installing?

Think it'll be too much of a hassle to return/reinstall so we might just paint it. 

its probably dried out and acclimatised and then appeared.

if you wanted a plywood wall then they should be fixing it, not you paining it.

As there are no perfectly straight edges to the horizontal stains, I'm wondering if these stains are a bad batch of glue, or poorly mixed glue where the various glue components have separated and not mixed together before use. Glues, like paints, are composed of various ingredients: an adhesive agent, additives (e.g. filling agent, resins, preservatives, moisturizers) and solvents. In this case the glues solvent, being of very low viscosity therefore able to seep through the wood particles, could be the culprit and is bleeding through leaving a stain.