AR Payment Foreign and Base Amounts are different in-spite of having same base and foreign currency

  I have encountered a very peculiar issue in our AR module.

We have an invoice in Canadian Business Unit (lets say CADBU) with Base Currency of CAD and LEDGER ACTCAD.

Payment came in for US Business Unit (lets say USDBU) with Base Currency of USD and LEDGER ACTUSD.

When accounting entries were generated then the payment application entries which hit AR and Cash for USDBU have different foreign and base amounts even-though the foreign currency is same as base currency (USD).

I have found that CADBU is not setup for inter-company entries. GL users handle inter company entries manually.

Any thoughts?