Though this is an old post an answer might still help - at least on the first question.
To get around this taskbar height problem I always open the offending skin in SS and set the title bar height to 23. The title bar dispays as designed but the taskbar then stays at the right height. Saving the skin will generate an error message, but I just click 'no" and all is well.
The other questions I don't know about, though I have suffered from the start button issues too.