I have setup my checkbooks to print the new signature. Why does the old signature still print?

Review the check format (Mekorma Checkbook Setup>Primary Check Format). Likely the original signature was added as a static image (logo) and you will need to either delete the image and add the new one as static if printing requires no threshold, or add as a Logical Field::Signature in order to apply Mekorma Security business rules for printing the e-signature.