Why would the Self AssessedTax code not follow the distribution from the line

We are running into a situation where they are entering the voucher and defining the Tax classification and the ship to and we are expecting it to follow the distribution from the line item that is being taxed and charge to the self assessed tax liability account. which is causing unnecessary inter-company transactions. I cant seem to replicate this issue in any of our QA/Dev environments however it keeps happening in production. I have attached a screen shot showing the issue