They are shadows that where drawn on the Exterior wall tiles, i remember spending ages back in the day trying to minimise these as i thought it was a BUG, Since back in the day i use PCKVIEW to export and fix graphics ( as BMPs) i didnt see the that the shadows where drawn on the tile graphics becuase everythign was BLACK anyway.... Fast forward to now, MCDEDIT shows transparent blocks as
Transparent so these SHADOWS now standout clear as day.
I removed the shadows from the Exterior wall tiles and re-saved them, fixed in 5 mins, i recommend you do the same on your master mod moving forward