I don't know what exactly is going on with my icons but instead of the app overlay for the roundness, the icons are now square. In the image below, google voice and alien blue is effected and i can i turn it back. i have tried fixing permissions, turning off all winterboard items and any other cydia apps.
Download/install fswipecache from cydia, just hit the icon on springboard and that should help clearing the cache of whatever theme you were using that caused that issue. Im basically having the same issue ONLY I choose a multitasking/folder background and the folder never changes, if I run fswipecache the multitasking & folder extension shows the background, just not when the folder is collapsed. So yeah you have a fix for that?