Ok, so I have a ridiculous amount of items that are not stacking in this game - including, as the subject states, and inordinate amount of non-stacked lesser soulgems. Then I have one stack of lesser soulgems of five - then like 25 that are separate. What is causing this? Can I correct it and force them to stack?

you can always drop them on the ground and take them back if you don't mind loosing their soul (if you do so they are not filled anymore) xD

Is this because some of them are stolden and some of them are filled with different sized souls?

I haven't tried that, does this happen when you put them in a container?

haven't tested in the latest patch, but in 1.1 they did lose the soul even if stored in a container.

I'll make sure I don't do that

Oh! So they show up separately when filled. That makes more sense, thanks guys!

They do the same to me when they become filled. I have like 10 commons in single stacks and like 4 in another stack. I can however store gems in a barrel and they hold the charge. They do not however decide to stack.

http://cloud.steampowered.com/ugc/630731953257721195/18CDB05634576FE91146A938E32101EC7D5C560C/

I believe whenever you claim a soul, the gem appears separately from any existing stack of filled gems. It appears that if you give them all to your Housecarl and then take them back, they'll stack up properly. Also, it seems that gems that are already filled when you find them have a different value and will not stack with gems that you filled yourself.

All pre-filled gems stack perfectly. Self-filled gems sometimes do and sometimes don't which is really annoying since oblivion. I do notice that grand soul gems don't seen yo be affected.

I had the same issue. They must have been filled when I took them off of enemies or something, because I don't have a soul trap spell.

On top of this all the gems seem to randomly move around whenever I use my inventory, there doesn't seem to be a true alphabetical order in them.