Commissions based on Collections issues when one invoice is paid by two Deposit Applications

We use the commissions on Sales that are eligible with collections and we have enabled the option of:

COMMISSION ELIGIBLE ON INVOICES PAID IN FULL ONLY.

In many of our fully paid invoices with 2 deposit applications, it is only considering one of those deposits as eligible commissions. For example, Invoice GUE5808 was fully paid with the following two deposits applications:

In the Commision Overview report this shows up:

We have a tax rate of 16%. So the transaction base amount is correct: 1,650 / 1.16 = $1,422.42

The calculated amount is correct: (1,650/1.16) * 0.25 = $3.56

However, the eligible total is only considering the latest deposit application GUE1900: (1,000/1.16)*0.25 = $2.16

It is not considering the first deposit GUE1899. We have several cases like this one.