It's shown in the WB config just above the skin thumbs.

UIS2=Magic pink used for transparency in BMP (No Png/Tga files)

Hmmm, that's odd Andrew, all my UIS2 skins have PNG's/TGA's in them, and BMP's as well.  I think you meant UIS1, correct?

Personally I set all my UIS0 skins to 1 star in Windowblinds and only see 3 stars and above, like you said, they are just Aero recolors.

I hope this helps and doesn't add to the confusion.  This is just from my poking around at SkinStudio.

UIS1 window frames - bmps with one set of options and a little different layout (e.g., LightStar's Innova skin)

UIS2 - bmps with a different set of options, and more options than UIS1

Per Pixel - the pngs

You can take a typical current UIS2 skin with the Per Pixel window frames and UIS2 frames, delete the Per Pixels sections from the skin, and it will use the UIS2 bmp frames for everything.  Of course you lose the png transparency and the ability to adjust the window frame transparency in WBConfig.

Some apps need the UIS2 frames - e.g., Photoshop Elements 2 will use the per pixel frames for the main window but uses the UIS2 frames for the image windows.  If there aren't any UIS2 frames defined it will use a default, I think Diamond frames (that's on XP )

Maybe that helps?

@Uvah- If you just want to see the differences in settings, an easy way might be to create a new UIS1 skin and a new UIS2 skin.  SkinStudio, "New skin" at left.  "Create new skin" window pops up.

"WindowBlinds basic skin" (1st item) is a UIS1 skin.  I see here too it says "They are the most compatible type of skin, but are more limited."  That might affect the Thunderbird app in OP.

"WindowBlinds advanced skin" (2nd item) is a UIS2 skin.

While poking around I also see that this is wrong:

I think I'm used to seeing skins where Diamond was used as a base and not changed.  Kind of looks like something has to be defined.

Also looks like a person might be able to make a UIS1 skin and add per pixel frames to it, not sure.

Good hunting Uvah.