I have the same issue. I changed the price Friday at midnight after a bookbub promo, Saturday morning it was still at $0.99. I sent an email on Sat morning, they responded 6 hours later saying yes, they see it shouldn't be price matched and it will be corrected in a few hours.
Sunday morning I went into KDP and updated price to $2.99 again. No change. I sent them another email but haven't heard back yet. It's ridiculous! Soon Kobo or someone else will match Amazon's pricematch and then I'll be going around in circles!
Not too sure what else I can do at this point.