Just curious, what is RAPD PCR? you amplify with a single primer?
For your cloning problems what is the enzyme you are using to cut the PCR
product? did you try to treat the PCR band with T4 polymerase to remove
extra As? are you sure your enzyme cut the PCR product?
Take a look at the recent paper in Nucl.Acid. Research for cloning of
blunt end products: Tari M. Haqqi NAR, 20, 6427 (1992)