I've confirmed that when I put soul gems in a cabinet in my house in Whiterun, they "lose" souls that they contain and show up empty again. I bought 4 petty soul gems, then searched the tundra for mudcrabs. I stored them in the cabinet. When I came back, two of them show up as empty. Thinking I was mistaked, I took those two and went to a dungeon. There I filled them and three more petty soul gems (as well as others) I found. As long as I had them with me, they held their souls. But when I put them in the cabinet in my house, left for a bit, then came back, they some of them were empty again - including - I believe - two of the lesser soul gems.

Frustrated, I grabbed the four that were filled and headed off to enchant some daggers. But when I got to the enchanters at the Dragonskeep, I found one of them was empty again! And I KNOW it was full when it was in the cupboard.

Am I the only one having this issue?

yes