I can't harvest souls anymore. I'm level 50 so i know how to do it.
I was walking along in places I've been before and noticed I was walking through clipped scenery. Looking back it was OK but I had walked through an outcrop of rocks.

I really don't understand how those two sentences are related? What went wrong exactly?

I harvested souls fine last night off Falmer in BR. Perhaps you're not equiped for it.

A. He can't harvest souls anymore
B. He's clipping through scenery.
They're related insofar as they appeared since the last patch. Get it now?

One more time ...

With the latest patch I can no longer harvest souls.
I am at level 50 and very familiar with how it works.

I have fully charged weapons.
I have a bag full of various size gems.
When I killm any size/type of enemy, nothing happens.
I do not get any messages such as.....
"soul captured"
"evaded capture"
"gem to small"

NOTHING

Use this thread to discuss the Patch

http://www.gamesas.com/topic/1341190-patch-14-unofficial-topic-4-with-changelog/

Note, your issue is more than likely mod related as I can capture souls just fine post patch.