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The following inputs could be useful for solving your issue:
1) For the month of Oct'10, run the Transaction register(default report is not in excel, we need to convert it) and also Material account distribution report(for inventory account). Using Pivot compare the quantities for all inventory items, the net quantities should be same. If there is a difference in the quantities between these two reports then the following could have happened:
a) Some of the receipts would have hit some account other than Inventory account. To find out which account the receipts might have hit, you need to run the Material account distribution report for all accounts for Oct'10. This happens because the assignment of account for items could be wrong.
b) Similarly check the Material account distribution for other accounts to find out if any inventory transactions have been posted to some other account.
2) Run Account analysis report for Inventory account for Oct'10 and find out if any Manual entries were posted to this account. Normally, all inventory transactions would hit the inventory account with source type as "Cost management". Please check for entries with other source types.
3) If you have loaded overheads like Material overhead, resource, labor, etc. then the ALL Inventory report would be valuing the material at Material cost+material overhead+Resource+ Labor. However, the GL account will not have these overheads, it will be with Material cost.
Please let me know after performing the above steps.