I have an item with multi-variations and Ki Markdown won't update its markdown

This is a known bug in eBay's system. We've alerted them to the problem and continue to ask them to fix it. Ebay's reference number on this issue is 160321-000010. In the meantime, the way to get around it is to make sure that the item is not on sale for one day. This will give it enough time to return to its normal price.