Right now, there is a contradiction on the logic of how WHMCS manages the Affiliate earnings when you have taxes.
For example, if you set up the option on the TAX SYSTEM:
"Inclusive Tax - prices are entered including tax"
THEM, WHMCS pay to the affiliates from the TOTAL *(including taxes),
We should not pay commissions for taxes we are going to pay to governments
But other wise, if you set up the other option:
"Exclusive Tax - Prices are enteresd without tax"
THEM, WHMCS do not include the taxes as "earnings" to pay to Affiliates.
And this is correct.
If you have taxes set up, its OKEY not to pay the taxes as "promotion" to the affiliates.
The affiliates should "Earn" only from the SUB TOTAL.
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