Business Area is different on Accounting document

Question

All,
The BA on GR/IR is different on accounting documents for material document (MIGO) and invoice (MIRO). Since the BA are different, I'm unable to clear GR/IR automatically. 
I checked the GL substitution rules and there are no rules associated with the GR/IR GL.
can someone please help. 
Thanks,
Sri

Answer 1

Thanks for your prompt response. We do want to keep BA as a criterion in automatic clearing. I have the following substitution rules
1) Vendor ABC and
    plant 85 and
   vendor recon GL 123456
   substitute with BA 47
2) vendor abc and XYZ
    plant 85 and
    GL 654321
  substitue with BA 43
the plant and divistion determination config is set to BA 47
The vendor on PO is ABC
the plant and division on PO is - 85
my FI entry is
Dr - FG (BA 43)
Cr - GR/IR ( 43)
when I traced the substitution rule it's saying true to Rule 2 above
why the rule is considering rule two as true when the condition is not fulfiling. 
FI enty at invoice
Dr - vendor recon (47) which is ture and the substitution is working
Cr - GR/IR (47)
How does the system derives the BA on FI documents. To me, it should carry the same BA through out all FI documents.
Your help is greately appreciated.
Thanks,
Sri