My problem appears to be slightly different now, the refining window is reporting 2/3 shard of vorpal, when I have 3 in my inventory. Otherwise the workaround listed appears to work sometimes.
Seconding this, I did manage to upgrade 2 rank 4s today but I can't create a Vorpal enchant and other enchant/runestone upgrades are reporting false missing materials. Interesting thing on the vorpal: I had 4 and couldn't upgrade despite everything being lit properly, then I put one up on the AH and now it's saying I have…