Hi Imran,
This is a common reconciliation issue:
Few basic checks :
1. Create Inventory value report ID to generate at transaction level along with Item, Item group etc..
2. Extract Inventory value report for the month where difference exists, You will get Voucher wise amount
3. Extract Voucher transactions for inventory Main accounts (Make sure you includes - Posting type)
4. You can first check in extracted vouchers , are there entry with posting type "Ledger" if yes then those transactions will not be available in Inventory value report because those are direct ledger entry without item
5. Do comparison of vouchers between both extracts and find the difference
6. If you are following moving average, look if this difference is due to purchase price variance account
7. Apart from this you can generate standard report which gives conflicts between inventory and ledger
