Deviation between the VAT specification and the total amount of all VAT accounts
Any deviation here indicates that the VAT report does not mirror what have been registered into the VAT accounts in the general ledger.
Note that the VAT report is based on amounts in the vat posting (VAP) documents. The VAT settlement is based on amount on the GL VAT accounts. To reconcile VAP against the general ledger, you can use REP/102356;YYYYMM where this filter refers to the VATperiod (not the accounting period).
Possible reasons for deviation
Previous VAT-period not reconciled. Compare the total amount on the VAT spec folder (PAR) to the balance of the VAT closing account. The deviation is most likely equal to the previous VAT period's VAT return.
No VAP posting have been triggered for a GL entry (ATR) with postings against a GL VAT account.
Make sure that the amounts per period on the VAT specification report are equal to the amounts in the VAT reconc folder.
If there are deviations between these amounts, search for manual entries in the respective GL account and reconcile VAP against general ledger in REP/102356. One can for example compare REP/102356 with ATRLIST;VATCODE:XX,PERIOD:YYYYMM in order to compare amounts in VAP with amounts in ATR.