If you open the console with /consoletoggle, the window doesn't have keyboard focus until you click exactly on the text-entry line at the bottom of the window.

Pressing Esc or the key bound to /consoletoggle doesn't make it go away either. You're stuck.

Yeah, there were some internal focus changes that messed this up. I'll try to have it fixed for this week.
It's somewhat related to the chat issue on this thread: http://www.vendetta-online.com/x/msgboard/2/29754

Should be fixed in 1.8.327