Im still having this issue in 4.0.4.
Was having it before the patch aswell so started a new save with the update, but the problem still exists.
I currently have 3 settlements showing 100% for both scrap collected and the time required to pass.
all 3 also have above 70 happiness, and the tracking "cities ready to upgrade" are tracking all 3 settlements. The 3 settlements are Sunshine tidings co-op, Tenpines Bluff and Red Rocket truck stop.