I can't help but wonder what the OP's default language is set to in the game or even out of the game while I'm thinking of it. Say for example you are in Ohio, so you speak English, and you install STO, etc. Launch, patch it and so on, then for whatever reason the default language is switched from English to say Japanese. The character set for Japanese isn't installed to the game so thus, you get question marks instead of what youtype. So I'd double check my settings in the Options IN-GAME. My gut is telling me that that's the issue, plus every time I've seen question marks when someone types something, it's ALWAYS because the default language isn't set correctly to the operating system.
Course then again, it could be anything... this is STO after all LOL