Do you see the correct characters being typed in other programs such as a word processor?

What version of Mathematica on which operating system are you using?

I would first suggest resetting Mathematica's preferences to installation defaults: 
http://support.wolfram.com/kb/3274

From your description, I imagine it could be a font corruption issue. Are you on a mac? If so, you may consider running through this tutorial which covers fixing a kind of font corruption that happens. 

If this doesn't help, I would suggest writing to support@wolfram.com with your license number or activation key.