Is is just me - or is the behavior of per-pixel frames using some sort of non-standard behavior for handling the sub-images? Interestingly enough, the program assumes the top and bottom borders are stacked vertically, even though the checkbox for stacking the frames vertically is not checked. Interestingly enough, checking the checkbox leads to some weird results.
I think this could confuse first time users, and the behavior should be noted somewhere.
. . . like the wiki the "Help" tab links to. Interestingly enough, I'd say over 90% of the links to the wiki in SkinStudio are unused. I'm tempted to just start filling it in, just so people have a place to go.
In addition, what is the purpose of the "Glass" entries? What exactly are they there for?