I've had that happen when my free disk space drops below or close to 1GB. It clears out the Webpage Previews folder in ~/Library/Caches/com.apple.Safari/ to save space and doesn't let it save the images until you get more space. If that is the situation on your computer, please try to clean up or move things to a different hard drive.
I did all that it's back now but this has happened twice since the upgrade.
Go to Top Sites, click on the "Edit" button and then you'll see at the bottom right corner options for "small", "medium" and "large" - you've probably selected "small" and this is why it shows so many small thumbnails.
It's simple: Safari opens the new windows at the same size that the last window was opened. So for example, if you closed a popup window, or something else lastly, the new safari window will open in that size.
Open safari, resize the safari window to really-really small. Then close the window. Quit from safari in the dock menu. Open safari. The new window will open in that really-really small size.