Hi Stef,
I was not able to replicate the problem of incorrect skin name with css handler, in my testing if I set specific skin on the home page (not site default) then when I go to pagelayout.aspx is shows the correct page specific skin name.
I do agree it is a bug about the IE specific css and the favicon, I have fixed those this morning, they are fixed now in the source code repository so they will be fixed in the next release. I also fixed it so that if CombineCss is false it correctly resolves the individual css file urls and uses relative urls.
Best,
Joe