Aperture thumbnails are sideways and half black

Lots of my thumbnails are sideways and half black. For example, a portrait photo will show accurately when opened, but the thumbnail is showing in landscape mode, but with the bottom half black. I have Rebuilt thumbnails, and even removed the entire thumbnail library and rebuilt it. In addition some of the thumbnails are all mixed up showing half of one picture and half of another. The underlying pictures however are fine. How can I correct this? I'm using Yosemite and Aperture 3.6.