From LedHed's Wiki
Fix Winterboard icons with black backgrounds
1) SSH to your iPhone
2) Change directory to /System/Library/PrivateFrameworks/MobileIcons.framework/
cd /System/Library/PrivateFrameworks/MobileIcons.framework/
3) Rename [email protected]
mv [email protected] [email protected]
4) Disconnect from the iPhone
5) Launch Winterboard and reselect the icon packages you want, then respring.