I've tried many different things and I have verified numerous times that the transparent pixels are properly saved in the png file, but a couple icons always show black where they should be transparent.
After being at this for a couple hours I believe I have found it to be a bug with Winterboard. It seems that if the icon filename starts with a capital letter (i.e. Icon.png), then the transparency stored in the icon won't be displayed properly and will be displayed as black.
I am having this issue with iBooks, Facebook, Shazam and Flixster, all of which have an icon filename starting with a capital letter. All the others display perfectly. has anyone else come across this issue?
I have an iPhone 4 running 4.0.1 and winterboard and have those apps, and am not experiencing that issue. I have renamed the AppIconOverlay.png and 2 other files that I can't recall the names of right now that were leaving a black rounded background on all my App store apps, including Facebook and iBooks. Is your problem with all App store apps or just the ones you mentioned?
It only occurs with icons with filenames that begin with a capital letter. I messed around with AppIconOverlay, AppIconMask, and AppIconShadow, all to no avail. In the end I had to resort to renaming the system copies in the Private/Frameworks )or whatever it is) and it solved my problem.
I am unsure why you are not experiencing the same issue. I am designing this theme to conform to Winterboard standards, so that I can disable summerboard mode.