I have encountered this bug as well, but hitting ALT+TAB to get to my desktop and going back seems to fix it. I take it to be a minor annoyance really, it's not that much trouble. Although I find it interesting that this is related to it locking out your keyboard. I was becoming frustrated last night when it wouldn't let me rename the city I'd just founded. The dialog box was there, but the keyboard didn't seem to work. Eventually I just gave up and I was able to rename it next turn.
Is it possible that this keyboard lockout happens fairly often? It happens to me a lot that I cannot cycle units by pressing "W" for the wait command. I end up having to go click on a unit manually. I don't know if ALT+TAB will fix that, it never occured to me to try.
I've also noticed that sometimes I have to give a go-to order twice before it "takes". Is this possibly because the first command wakes the unit from its fortify status and then only the second command actually moves it? Can anyone else confirm this?