I used the free choice pack we got in the last patch to get a R15 Empowered Runestone. Since it's account bound I wanted to sell one of my non-account bound R15 Empowereds because I don't need 7. WHEN I UNEQUIPPED THE UNBOUND RUNESTONE IT STACKED WITH THE BOUND ONE AND NOW THEY'RE BOTH ACCOUNT BOUND!
EDIT: So I played around with this a little more, and the bug isn't what I originally thought. When inspecting runes that have already been slotted into companion equipment the tooltip doesn't tell you that it's bound. It seems my runestones were ALREADY account bound (i just forgot because I've had them so long), but the only way to SEE their bind status is when the runestones are directly in a bag in my inventory. Inspecting the runestones in their companion equipment (which can be either equipped to the companion OR in the bag) will not tell me they are bound. Sorry for the confusion.