Your screen shot shows an admin page hosted in a narrow skin and overflowing the pane. If the problem happens on non admin public facing pages it would be more of a problem, but a narrow design can have this result whether the skin is generated by Artisteer or by hand coding. My recommendation would be to make the design wider, it looks like it is optimized for 800x600 but these days that is narrower than it needs to be. 0% of my traffic has screen resolution smaller than 1024x768. Wider skins are better, with very narrow skins you end up with side columns that are too narrow and the page becomes crowded.
In any case it is expected that in a few cases you may need to tweak the css to fix issues like this.
If the problem happens on non admin pages, you can send me a design or skin that demonstrates the problem and I will take a look. joe dot audette at g mail dot com
I will work on the vertical menu support as soon as Artisteer releases the next non beta version.
The issue about the broken icon was reported on another thread and will be fixed in the next version. For now a workaround is to copy the file /Data/SiteImages/wrench.png to the root.