I'd suggest you try some troubleshooting steps.
Your sidebar has lots of small problems. It has empty
<ul> (unordered list) and the page list itself is not wrapped in a
You have found with other themes that things work, good first troubleshooting step! So the next thing you can do is copy the sidebar from a theme that works, and put it into your theme (backing your original of course).
Then see if the problem persists. If it does, then it's not the sidebar (and you can start wondering about permalinks, etc). However, my suspicion is that it will in fact be the code in your sidebar.
Go through the sidebar that works, comparing with your sidebar, and you can either amend the working one to fit with your theme, or you can try and locate the problem with your current sidebar.
Troubleshooting is a series of attempts to isolate a problem. I feel your pain though, it would be ideal if someone could fix it for you.
Best of luck,
interesting site by the way. i had no idea that kind of stuff existed.