Use Source orb essence of lowest quality. It needs to say x essence not great or alien.

Soap+Source orb should work. Did you try without a crafting station right?

I'll try again. I have two regular orbs so I'll try either one and see if one or the other is bugged somehow, will advise. Also I'm using lowest quality essense as well.

Tried the following combos without crafting station:
Regular Source Orb One+Regular Air Essence+Regular Earth Essence=Invalid Combination
Regular Source Orb Two+Regular Air Essence+Regular Earth Essence=Invalid Combination
Regular Source Orb One+Reg Life Essence+Reg Shadow Essence=Invalid Combination
Regular Source Orb Two+Reg Life Essence+Reg Shadow Essence=Invalid Combination
Regular Source Orb One+Soap=Invalid Combination
Regular Source Orb Two+Soap=Invalid Combination
I had no fire essence to test with unfortunately.

I tried different individual essences from the stacks one at a time with no luck and different bars of soap as singles, like the essences, with no luck. I think I'm bugged. I have the following mods in addition to your own: Free Pet Pal and Fast Run. I've had no problems with other crafting combos. I've got the latest patch.

Can you send the screenshot of source orb you are using? As far as i know source orb has only one type. Tarquin sells it for example.

Here you go:
http://s90.photobucket.com/user/wreckless_01/media/Source%20orb%20One_1.jpg.html

orb seems fine, do you use steam version of the mod? Any chance you are using older than V 0.94?

I'll check and see if I'm up to date. I'll just update to v .95 and see if that helps.
Edit:
OK, upgrading the v.95 it made the transmuter. I think I was running .91 and that was the problem. Sorry about that but thanks very much for your help and the mod!

I'm having trouble with the Ruin of Uniqueness. I made the Transmuter though.

Show me the recipe screen with ingredients for crafting rune of uniqueness.