Clearing Thumbnail Cache = Missing Images

It seems everyday I am having a new issue since I upgraded. Tried adding some images to the site for my main category image in several categories. They aren't showing up so I cleared the thumbnail cache now 90% of the images are not showing up for products within the categories.

So maybe it is just taking a (long) while for the library to rebuild as some images are starting to show back up. But still not sure why the images I am adding for the categories isn't showing.