AP AR Distributions are incorrect

Summary:

AP AR distributions are not derived correctly for manual transactions.

We have a supplier and a customer for intercompany AP AR process.
We defined intercompany customer and supplier association.
Intercompany AP AR is working as expected. but the issue is when we create a AP manual invoice/AR manual invoice for the same Supplier/customer which was mentioned in "intercompany customer and supplier association", the accounting distributions are derived wrongly.
We are expecting liability and revenue account to derived which was there on supplier and transaction type. But system is deriving from intercompany balancing rules.

How do we stop system considering intercompany balancing rules for manual transactions?