I have the same problem and have played with several settings with no luck.
I'm running an iPhone 4 w/ iOS 4.3.3 (redsn0w). I did a Cydia update yesterday and, after a respring, all of my icons had disappeared. Including my folders on the springboard. After some playing, I got the icons back but they weren't organized properly. When I selected one to move it, it disappeared. All labels are present, just no icons. Here are some notes:
1. As booted, all I see are icon labels. When the screen is first painted, like when I first swipe to unlock, I see the Winterboard background before an opaque overlay is drawn with the icon labels.
2. I rebooted in safe mode and everything is drawn fine.
3. Resprung out of safe mode and it's back to being hosed.
4. Using 'sbsettings->mobile substrate addons', I disabled the following components: FolderEnhancer, Iconoclasm, Gridlock, IconSupport, FiveIconDock, MultiIconMover and Shrink. Basically everything that seams icon or screen related. Now I see all the icons but when I try to move them, they still disappear.
5. My next steps will be blind stabs and experimentation so I'm hoping someone might have better insight to lend.
Thanks for any help.
Andrew