Recently I moved to the Tiger skin and found that when subfolders have images with duplicate names and set for folder thumbnails only the last one is used for displaying the thumb. It's because every folder thumbnail goes to "thumbs\folder" under the output directory and replaces the previous one with the same name.
OK, maybe that's a behavior I didn't notice when I was using the Turtle skin for my aggregating album - I output all my albums as subfolders of a single folder then I build an album for these output folders only as indexing album. As you know Canon uses only four digits for naming and this way happened duplication for the thumb images. Anyway, I'll workaround with some rename of files.
Yes, this proved to be a poor design choice to use only 4 digits, like IMG_0001.JPG, but that time many OS's were able to use only 8 digits as file names, plus 3 as extensions. No one thought you'll have more than 10 000 images in your whole life. Using folders - based on dates for example - to sort out large number of images might help.