You can overwrite the Excise material type maintained in your Material & Chapter id combination. Irrespective of the Excise material type in J1ID, System takes the MIGO/J1IEX Excise material type provided it is changed in MIGO/J1IEX.
You said there is an accounting entry for your material document for excise. Check the excise material type assigned in your material document under Excise item tab. If it is RG23A/C then you would get the accounting entry provided cenvatable tax code was used in your purchase order.