Upon further examination, the glittering eggs seem to have taken but not the Handicrafted egg. I'll probably file a ticket for that since I have no idea why that in particular wouldn't count when the glittering eggs seem to work fine.
The issue I was having was that first I noticed after using the handicrafted egg that it didn't count.
So, I hovered over the glittering egg khara as I used a glittering egg to watch the counter go up, didn't know that it doesn't work that way and you have to click away and back to the khara to see the count go up.
So now on my rogue (with 49 or 50 active khara ) it still shows no used Handicrafted egg, but 2 used glittering eggs.