Redo the whole icons because of some bugs. Only for Iphone 4. Some of the icons will show up with a dark border around them, this is because of the files responsible for auto-skinning.
To show the icons as they are intended you need to find these files and rename them. **Do not delete these files, only rename them**
Navigate to: /System/Library/PrivateFrameworks/MobileIcons.framework
AppIconMask @2x.png
AppIconOverlay @2x.png
AppIconShadow @2x.png
Rename these three files by putting a "1" in the name so that it looks like this:
1AppIconMask @2x.png
1AppIconOverlay @2x.png
1AppIconShadow@ 2x.png
Some icons not changing? We need to wipe your icon cache! Navigate to /var/mobile/Library/Caches and delete this folder (yes, the entire folder):
com.apple.IconsCache
Reboot for the changes to take effect.