I noticed that problem as well, though I'm not really sure how to go about fixing it ^^;
I can think of two different ways. Whatever single pixels that are black will be the exact same color on every stock skin, so you could probably cross reference it and maybe throw some random pixels in the likely areas to see.
It's also likely that there is an XML file that checks specific pixels on the skin, but I wasn't able to find that file.
I did some comparing myself, and it could be just my copy but I noticed that there are some artifacts and whatnot on the two color blocks. (Top left and bottom middle) on your version compared to the original. I wonder if that's a consequence of the format saved.
Edit: I repaired the artifacting of those color chunks using the save format "8.8.8 RGB 24bpp unsigned. I noticed extensive artifacting elsewhere in the image too that was likely unintentional. I'll see if this save format is recognized by Mabi, it may end up being a better option.
Edit 2: that didn't work. It prevented further artifacting but unfortunately the colors weren't fixed. I had to change to 8.8.8.8 ARGP 32bpp unsigned to prevent some issues though.
Edit 3: I found the associated xml file \data\db\themepack\
I've yet to figure out what line is the associated box, but I'd wager it's a line that doesn't have it's own patch defined.