I'm also experiencing the same problem as the OP. I'm converting epub to mobi using Calibre. I've done many books this way and never had a problem. In the debug folder, everything looks fine. It shows up fine in the Kindle Previewer app. But on the actual Kindle, some of the images display strangely, exactly as described. Here are photos so you can see what we're talking about.
Kindle screenshot:
http://dl.dropbox.com/u/38282222/screen_shot-19089.gif
Actual jpg:
http://dl.dropbox.com/u/38282222/Fig7-2_fmt.jpeg
I'm going to try converting my jpg images to png as John123 suggests.
Sarah