Can any body explain why the system is showing different values for the same iput values like Doc type WE , Co code ,Business area and posting periods in the both transactions like S_ALR_87012344 and FBL3N
If the account(s) that you're running both reports for do not have line item management enabled in their master data then the balance of S_ALR_87012344 will differ from FBL3N. This can also happen even if the account has been changed to line item managed after some postings were made. Check if "Line Item Management" is enabled for the account using t.code FS00 and also check the change history for the account to see if this field has been recently changed.
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