Common causes for discrepancies between the GL and subsidiary reporting include using non-tangible parts (type N, L, T) assigned to Item Classes that post to the inventory GL Account and/or tangible parts (type R, M, A & F) assigned to item classes that post to expense or other non-inventory GL accounts.
 
You need to look at the GL Account assignment in SM-C and the types assigned to inventory items.
 
Also, items received from PO into QC are not on the Inventory Value report but are included int eh GL Balance so the PO-J-B report needs to also be considered.
 
If you do not have the IS Tech enhancements doe DBA Classic, then there are other types of entries that can be made (such as changing an item cost in IN-K) that affect IN-F but do not post any sort of transaction or GL Posting.  You also can not (without the IS Tech updates) run the IN-F report to get the inventory value as of a prior date.
 
As for the actual COGS number used when invoices are posted, timing is very important.  The invoice posting uses the Average Cost of the items on the invoice at the time the invoice is posted using SO-G.  If invoice posting is processed before the work orders making the product are completed then the parts are being shipped before they are made (as far as the system is concerned) so it doesn't know the costs.
 
If you would like more specific suggestions, we would need to look at your data.  DBA may no longer support the software but we support all versions, with or without our enhancements.