I am curious if Killbeam finally determined the cause/solution to his issue in his initial post.
I am a new player of this mod. I have only played it a couple of days. But that was after several days of reading about the mod and watching Kinggath's Tutorials. And then spending a good day installing the 3 in 1 Sim Settlements mod and researching and selecting which add-on packs to try out. For someone new, there is a lot of information to get through in understanding the mod and I had reached information overload a couple of days ago when I decided to dive in and just try the mod in a playthrough.
Using the RotC city plan, Sanctuary reached 100% ready to level up with no option to level it up at the planning desk. Upon checking I saw that the settlers had collected 0% upgrade scrap at which point I re-watched the Upgrade Tutorial to make sure I had not misunderstood that they would collect it automatically over time. I then started googling and found this thread.
Kinggath's reply to this thread was very informative and helpful. So I went and checked the only two other cities I had started that had any time upgrade automatically. The first was Tenpines Bluff, a small agricultural settlement. Tenpines Bluff was 78% to next level with 0% upgrade scrap. The second was Starlight Drive-in. To my surprise Starlight had upgraded to level one in my absence and was 6% to next level with 0.4% upgrade scrap collected. I did not do anything to nudge these city plans along and just let everything happen automatically.
Referring to Kinggath's reply to this thread, I observed that both Sanctuary and Tenpines had created agriculture only settlements whereas Starlight had a mix of agriculture and industry. So it appears that in the installation of my game the automatic upgrade scrap collection is only working in the presence of industrial plots.
Please let me know if this matches others' experiences or if I have overlooked something. I have not yet tried the workbench scrap uncapper mod but I am considering trying it to see if it has any effect.
