This is a long-standing Kindle firmware bug: eInk Kindles don't support embedded fonts for AZW3 books with RTL text. Or, more precisely, they support them, but they don't display the proper initial, medial, final and isolated glyphs.
If you have an older Kindle or if your firmware is 5.8.7.0.1 or lower, you can
jailbreak your Kindle and install a font hack, which'll allow you to override the ugly default font with your favorite Persian font.
If you manage to jailbreak you Kindle, install the
font hack and override Code2000.