Sorry Rubx, I don't have that issue.
For the record, I play around with System bits and piece very RARELY. I do it sometimes (for example, I edited the 10.5 keyboard extensions to give me four finger gestures), but when I upgrade, I tend to reverse the edits before updating. I don't add crazy extensions, so for me, most things work, if there's ever a bug, chances are more people experience it.
That said I'm getting to the bottom of my iPhoto/System Preferences issues. It must be to do with the number of images. I have around 80,000. Furthermore, there is something inherently different between the Desktop pane and the ScreenSavers pane, as ScreenSavers EVENTUALLY loads it when the Desktop pane does not.
A workaround at the moment is to close System Preferences on the ScreenSavers pane, so when you open it again, it defaults to ScreenSavers, preventing the Desktop pane trying to load it. Once the photos have loaded in ScreenSavers, then switch over to Desktop, and they were all there for me.