What file format are you scanning/saving to? BMP or somthing 'uncompressed, i.e. NOT .jpg ???

For clarity i go with .BMP at the expense of LARGE files.

Also try reducing the colour-palette in your final pix, since the BGlass artwork aren't photo-quality (millions of colours) and something similar to cartoon quality, you could reduce your colour palette from 64million colours down to 256 colours with no image degradation.
This would reduce a LARGE file into a relatively small(er) file to worjk with, especially if you have RAM limitations.

Reducing the colour palette may also help reproduce the exact colours on your BackGlass.
If you scanned a uniform yellow area on the BG, you dont wan't to be working with 100's or 1000's of shades of 'that yellow' in your final scan.

food for thought 
MM.

Thanks for that Marty,

Yes was saving files as .jpg but wasn't that happy with the results even at 600dpi so will try again with what you suggested later today