I have a custom resource pack with a custom 32x HD font (located in "assets/minecraft/textures/font/ascii.png").
The font is displayed correctly if loaded for the first time from the game menu. The moment you exit the game while your resource pack is still loaded - the next time you launch it, the letters are kind of "misplaced" (check the attachment). The only way to fix it is by switching back to default res.pack, restarting the game and again loading the custom res.pack from the menu.
(Resource pack that I'm using: http://goo.gl/QtyA7 )