PLT files are great once you're familiar with them, but many things about them are very tricky at first. I think I have a fairly good guess of what happened to you, going from my own initial experiences.
PLT files do not support transparency of any kind. If you edit a file using selections with fuzzy edges, then when you save the file the plugin will fill in any element of transparency in any pixel with solid black. Accordingly, never use anti-aliasing or feathered edges when making selections, as they tend to leave ugly borders around selections (which you only see once you reopen the image after saving it). If in doubt, sharpen your selection.
A few other facts about PLTs...
Each and every pixel can only have image data in one layer. Anything you paste into a higher layer will override what is in a lower layer. Once you save, close, and reopen a file, anything you might have had in lower layers that was covered over by image data in a higher layer will simply be gone.
Most colours in the palette translate pure white (255, 255, 255) in a PLT as shiny chrome in the game. In the case of some PLT objects, like clothing icons and cloaks with transparency enabled, this will make those pixels transparent. Unfortunately, though, this doesn't work with body parts - and PLT Editor (the one that shows the various layers as different high-contrast colours) changes the values of some bright colours. Namely, it turns the very brightest few colours in the Leather 2 layer (bright yellow) to white. It also turns pure white to a colour just slightly darker (254, 254, 254), thus ruining the transparent background of clothing icons.
Anyway, enough of that for now. I hope that helps. Please feel free to ask any other questions if they occur to you.
Modifié par Estelindis, 07 février 2011 - 12:02 .