I have the very same issue.
Ive been searching the net for a week now and still cant find an answer.
Ive added this to the info.plist with-in springboard folder and also for the apps:
<key>UIPrerenderedIcon</key>
<true\>
then replace the info.plist for the original, Delete the icon caches, located at /private/var/mobile/Library/Caches and respring, - never worked for me.
Ive also changed the image SBGenericAppIcon.png in springboard folder incase it was the original being overlaid but doesnt seem to be.
I cant find anything else to try upto now. Its starting to do my head in a little bit. I installed winterboard and it got rid of the shaddow thing straight away so would love to know what it does. When i removed winterboard the shaddow came back.
