This is what was happening:

A register transaction is started and the custom tender was launched (TenderActivity)

The custom tender would temporarily malfunction.

The cashier would take card from the customer and put it into the clover hardware. The custom tender would still be on the screen, but In the background the clover hardware processes the transaction and marks the order as PAID.

While step 3 was happening the custom tender would recover and mark the tender was having paid the amount.

This causes the TenderActivity to mark the payment as complete with the full amount plus tip if present.

Clover says the order has already paid because payment was taken on the hardware in step 3, marks the new payment as a SPLIT_CUSTOM and includes the tip if given. The amount paid by the custom tender is marked as 0.00.