Kindle Fire: Why are my mobi files showing up as documents?
You just finished moving your collection of .mobi files to your Kindle Fire only to find that some of them ended up in Documents instead of Books. It turns out that the reason those files showed up as Documents is that they contain a personal doc tag that tells the Fire to place them in the Documents directory. Here’s how to remove the tag so that they show up as Books.
Step 1 - Connect your Kindle Fire tablet to your computer using a micro USB cable. Move (not copy) the problematic files to a new directory on your desktop.
Step 2 - Launch Calibre (if you don’t have it installed, go here, download the application and install it).
Step 3 - Once Calibre opens, go to the top menu bar and click the Add books button.

Step 4 - Browse to the directory on your desktop where you placed the files; select them and click the Open button.
Step 5 - When the Calibre Library has completed the import of your .mobi files, select the files and go back to the top menu. Click the Convert books button.

Step 6 - In the upper-right corner of the Convert window, click the Output format dropdown button and select MOBI.

Step 7 - Go to the left pane of the Convert window and click MOBI Output.

Step 8 - Go to the right pane. In the Personal Doc tag textbox (located under Kindle options), delete [PDOC] from the textbox.

Step 9 - Click the OK button.
Step 10 - Wait for the conversion process to complete, then move the converted files to you Kindle Fire. Disconnect the device from the computer. Your files will now be listed as books.