When you create a bootskin, you create two images, the background image, and the progress bar image. As you may know. And these images should have the same palette - because when the bootskin is actually displayed during a reboot, only the Progress Bar image palette is loaded and used for both images.
Now, with that in mind, let's examine the palette. Many, if not the vast majority, of image editing applications ( MSPaint is the worst ) set up a sixteen color palette with Black in color slot-0 and white in color slot-1.
This sucks if your image isn't using black and white, because you just got robbed of two color slots, which matters when you only have sixteen to begin with.
OK, to the question at hand. During reboot, the prog bar image moves across the screen and behind it leaves a trail. This trail will be the color in slot-0 of your palette!
So, to blend in the trail with the background, you need to manipulate the palette and image so that the background is the color in slot-0.
My Bootskin Buddy gadget allows you to set the values for palette colors (but does not do actual image editing, per se ). You may find it useful. Also, thew demo bootskins included with that gadget demonstrate this non-black trail solution. http://www.deviantart.com/deviation/30733603/