If your Pre-Tax Deductions setup in KeyPay did not have a bank account attached and were setup to be paid manually then the split will not come through the import done via Agrimaster. In this case, you will need to create a manual transaction for that Pre-Tax Deduction.
If you would like it to be automated for a split transaction via Agrimaster then you will need to attach a bank account to that particular transaction and the future splits will work. Adding a bank account now will not apply changes to pay runs already processed.
Contact KeyPay Support for more information.