Currently I'm putting all the books and comics I want to read and the media (video, music) -- all on my SC card. I don't usually read more than one thing at a time so I can delete material from the card when I'm finished and add more later on. I've downloaded a lot of free and a few paid Kindle books to my computer to see on Kindle for PC, but I every week or two I copy them to a separate file and run 'em through Calibre to turn them to epub, which I can back up to CD (to save them), then read with either my Tab off the card or my JBL off internal storage (it's faster that way on the JBL).
So this is another option. If the Kindle app is giving you problems, change the book to a different format that you may have a better app for. I figure there are always at least two ways to approach a problem.