I went out today and got my radon monitor and then got up on the roof to troubleshoot this siding on the upper level with the mystery marks.
I could not feel any nail heads under any if the stains and I pulled the ends to see if underlayment was installed and indeed it was. I also felt behind the siding at the ends where stains were close to the ends and no nail head locations correlated to stains
Next I looked up under the edges and found that there are in fact weep holes every 16 inches and over the stains.
Winner winner chicken dinner For Team Larry who were on the drainage theory. Honorable mention for Team Jr because similar marks can be nail-head related so we should always check that, too, when marks like these are observed.