I have not faced the same issue in Standard Database. But I am sure that the issue is not related to any bad customization, because there is no such kind of modification in posting routing.
If you’re not able to reproduce the problem in the standard demo database, then it’s very difficult not to say that the reason might be your customization!
But let me suggest that you use the debugger and very detailed check what the differences are when you post a output journal where it hit the item ledger entry table correctly and one where it doesn’t. That would answer you why it goes wrong.
If we want to update Inventory level for a finished Good Item through an Output Journal than we have to select the last Operation No. (from the Operation Sequence of Prod. Order Routing Line Screen) in the Output Journal Screen otherwise inventory will remain same only Capacity Ledger Entry will be happened.
output journal is for adjustments like time, scrap, output quantity, not for playing in inventory. It hits, however, inventory when you finalize you operations and mark Finished in the output journal.