HELP! Light brown marks keep appearing in at the top of newly-painted walls

[Elizabeth Rose]

We recently bought and rehabbed a standalone Philadelphia townhome - the city knocked down the townhomes on either side about 5-6 years ago. We replaced the old roof as part of the project and had the interior walls primed (with Kilz) and painted. 

A few weeks after painting, light brown marks appeared at the top of some of the top corners of a few of the walls on both sides of the house, upstairs and downstairs (not the ceilings, just the tops of the walls). We painted over the marks, thinking the discoloration was from leftover moisture that was let in by the old roof, but the marks have come back. Our contractor is unsure how to fix the issue, so I would love some help troubleshooting.

I had the roofer come back and check the new roof - everything looks solid and the party walls are capped and sealed. 

There also doesn't appear to be any cracks in the exterior stucco on the sides of the house.

Any idea what may be causing this? Or what type of vendor to call in to fix it? Thanks in advance for any thoughts, advice, recommendations!