Cleartype \ Antialiasing does not work in per pixel frames in WB.
I have clear type and anti-alisising enabled with my fonts in both regular and per-pixel frames...and they work fine.
nickdc, are you saving the changes in skin studio? If you don't save, your changes will not show up when you re-apply the skin.
It sounds like you are using skin studio 6...if you are, I can't tell you all the steps necessary to change fonts. I am still using version 5, and I think things are done differently, as far as making changes.