If the console doesn't even display the welcome message maybe see (in Xcode preferences) if the font you are using somehow became corrupted. Also see what foreground color you have assigned for the font and that it isn't a white color. If you click in the console window is there text that is not visible but that you can select?
If so, try Cmd+C and paste it in TextEdit maybe. Also try switching the debug prompts to another font. You will find the settings for switchings those prompts under Xcode prefs > Debugging in Xcode 3 and under Fonts & Colors, I believe for Xcode 4. Even though you did re-install I can't remember if the preferences plist will get deleted in the re-install. The Xcode preferences plist should be under ~/Library/Preferences/com.apple.Xcode.plist. Try renaming that file temporarily before starting up Xcode.
If the console does display the welcome message but you get no output from your program see if you are using an NSTask and setting stderr to be used for your own output. I had this happen once but I was also using SenTestingKit at the time to do my unit tests and somehow it ended up to where noone was able to print to the console - not my cli program and not the testing kit.
As a last resort, Xcode 3.2.4 is out since a few days.