After 1.0.6 I was able to craft only 2 runes. I dropped all my other runes while crafting them and picked them back up hoping that it would register them properly in my inventory...... and the answer is a big fucking nope.

*Sadpanda*

how does it register them?? i havent heard of this bug

There are several types of runes - greater and two lesser. In theory three lesser are supposed to be reforged into one greater. Problem is, all old runes (I think ones we acquired before 1.05 patch) are not registered as properly usable, and only those lesser runes we crafter are usable for upgrade.

Rudy is correct. Only the runes that you craft can be upgraded by crafting diagrams. The ones that you find / buy / steal are not craftable.

Kinda of.

You can buy runes and they can be upgraded. However, there are usually two types of lesser runes. Only one of these can be used as an upgrade. The item list for the command console shows two types of lesser runes.