So, visually the pictures look bigger? It's not that the folder containing the files went from being 2 MB to 8 MB?
I'm assuming that this is not a special piece of software you're running - it's the "My Pictures" slideshow in the screensaver menu, correct? If you go to the "settings" for that option, there's a scroll bar that dictates how big you want the pictures to be. You could try playing with that. There's also a check box to "stretch small pictures". See if that's on or not.
If that stuff doesn't make a difference, try changing your screensaver to something else, and rebooting. If that gets rid of the warning at startup, change your screensaver back to the slideshow, and see if it's fixed or if it causes the error message to appear again.
That should at least help you figure out what, exactly, the problem is.