That's interesting.
I have scanned chips in the past, and those came out fine. I think it works better if you can save the scan as a .gif file; .jpeg files always come out with the white background on them.
I have also done some custom chips and used the files that I created in Photoshop. I saved those as .gif files too, and now I have images of my custom chips as well. If you have Photoshop, you can also take your scans and work on them that way (it might also be possible to use Photoshop Express as well, which is free, I think...).
Good Luck.