Wedge

The first problem is a common issue with absolute positioning and z-index stacking.
Basically, there are two ways of fixing it. The first isn't possible because it involves removing positioning from sortable elements, which completely breaks the feature. Uh. The second implies moving the select box out of the current flow, for instance by putting its HTML at the very bottom of the page, outside of the #wedge div, etc. This means it gets its own z-index stack, and will correctly show up everywhere (see alert popups, for instance.)
Unfortunately, doing this has a MAJOR problem: it forces me to absolutely position the select box dropdown in pixels from the start of the screen, so if the select box ever changes its position (e.g. hardware scrolling when opening a hidden sidebar, or doing any kind of animation such as showing/hiding the header) will not update the dropdown's position, meaning it will, quite simply, stay where it was, and show up in silly places.
I tried doing that a few times in the past, and always gave up.
Another solution could be to change the way the sortable list is shown... For instance, I could show the current setting with a button next to it (change), and clicking it could open a popup when you can choose your preference. That's pretty much a cop-out, and a usability nightmare I'd say.

I don't know what to say, or what to do... What do you think?

As for the second problem, I'll look into it.

Have you tried using the Purge Cache menu option after changing an option..?