Does the sill flashing void the warranty on the windows when you install it and do away with the shims?
Did they check the deck columns at the stucco house for moisture? They are next to impossible to make water tight!
Was there a moisture barrier under the EIFS?
Did the backer rod and sealant joint go back to the sheathing or did they run the first layer of foam up tight to the windows and just leave the joint in the trim application?
If the top of the bottom window had flashing instead of a backer rod and sealant joint some of the water might have been kicked out.