Costing workbench behavior has been unsteady for us since we upgraded to kinetic from Epicor 10 where the only complaint I had was with it’s speed and memory use limits on the server.
We just encountered new behavior (again) on 2025.1.2 that is (of course) ‘working as designed’.
This one involves the View As Assembly (true/false) setting for each BOM items.
View as Assembly (to my knowledge and I go back to Vantage 7) was a ‘convenience’ choice for us in that you could drill into the the mtlPartNum and see it’s method in the old Method tree views. It had no impact on planning, costing & job detail generation.
On 2025.1.2 it suddenly starting impacting rolled costs much the way you describe (leaving out whole sub assembly costs even though job details generate clean as expected and job estimated costs are what was expected).
I’ve found the inconsistent behavior disappears by ALWAYS having it set to false.
I cleaned up a little over 100,000 BOMs with DMT, have an intneral IT request in to customize so it defaults to false, and for now, continue to clean up new BOM entries with DMT daily before cost rolling new items.
I vaguely remember and similar issue for another early version of kinetic but can’t recall which one anymore.
You may want to try playing with the pull/plan and view as assembly BOM material flags to see if it’s a similar issue.