I’m having a similar problem. I’m using a bulk discount plug in as well and when yours applies it wipes out the other discount. https://www.ads-software.com/support/view/plugin-reviews/woocommerce-bulk-discount#postform
Also when the discount goes to the default payment method you have to un-check and re-check for the discount to show up.
I wish I could be more help. Hopefully you can figure out a fix.
