AP Intercompany transaction

We are on PS 9.2 , PT 8.54. When Generating Journals in AP in the situation where a discount is taken on a voucher that also involves an intercompany entry (the company booking the expense is not the same as the company from which the checkwas paid) an extra line is automatically created which then causes the entry to be out of balance.  When the account for "Interunit Ops Receivables" is used it somehow triggers the extra line to be added to the journal entry for the same credit amount but in a different account thereby causing the entry to