The printing quality of the 3rd series is significantly lower than the other three rerun series and examination of Topps Vault auction items indicate that there are two reasons why:
With regards to color separation techniques, the color negatives that were auctioned by Topps Vault were different for 3rd series than they were for the other rerun series. Instead of the typical 4-color CMYK negatives, as seen with the other series, they auctioned only 3-colors, which is a CMY variation wherein CMY color saturation is used to create the black tones. Although black ink was still used in the printing for the borders and copyrights, there is little or no black in the images themselves (most black text is green). This 3-color technique may also explain the over-saturation of color in the cards.
The evidence that Topps used stickers as the basis for the third series re-issue images arose when Topps Vault auctioned what they called "Shock Theatre"/"Wacky" card paste up sets in April 2004. These auctions consisted of a Shock Theatre card with a Wacky Package glued to the reverse of the card. The auction descriptions stated that these paste up cards were used to create the 3rd series reissue "checklist sheet". Close examination of these stickers revealed that these wacky stickers were used as the basis for the images themselves and were not just for checklist verification.
Depicted below is a side by side comparison of the "Shock" sticker from the Topps Vault auction along with a re-issue Shock card - note the printing errors in the 12th series card: the diagonal line under the 'K' in SHOCK and the off-color donut spot at the 10 o'clock position near the right-most "punch-hole" at the top of the card. Both of these printer defects on this particular 12th series sticker also appear in the 3rd series re-issue card.