I've run into an unexpected issue with manual payments: when checking out, discounts are successfully applied on the front-end (discount amount is returned and total amount updates accordingly) but when viewing the order in the Store admin the discount is missing from the order (i.e. displays $0.00).
This does not happen for credit card orders (processed through Stripe).
A note on my checkout process. I'm using Switchee to check the member group. If the member is in our commercial member group they're presented with a manual payment form so that we can process the order and invoice for the payment.
I'm at a loss for what may be happening during the payment processing that would drop the discount. To be sure there are no conflicts, I disabled the two extensions that I use in conjunction with Store (one hooks into store_order_taxes and the other store_order_complete_end), but still no luck.
Has anyone encountered this, or something similar?
Thanks in advance for any insights.