Could you turn on individual settlement info on the HUD and see which settlement(s) do not add up correctly? It will only check what is in each individual settlement as you walk in, not all settlements each time.
@kinggath maybe we could change it so every 24 game hours it does a loop and checks all settlements? It's only checking numbers in the datastore, so it doesn't require the settlements to be loaded. We should also put in a check to stop it from running if the ClearStoredExcessCapacity array is not empty (we don't want it running in that two minutes the player has to fix up their max storage before losing resources).
If you've found a way to pass on a save
@yaugie that would still help.