How are you loading the books to the Fire? Whispersync download from Amazon? Sideload? Are the books official Amazon books or are they modified books? Does the fire sync any information for any book, or is it not syncing anything for any book including Amazon books you DL through Whispersync?

Sorry for all the questions but these help us see what the problem might be. You might consider doing a reset/restart of the Fire. Sometimes that helps clear out certain issues. To reset hold down the power button for 20 seconds. After the Fire shuts down you might need to press the power button again to restart it.