I've suffered this problem many times and so do my colleagues
Sometimes after you stroked some keyboard and mouse combinations this behavior showed up : you have to click a xterm's title bar to focus on that term so that you can input, instead of any place in that window.
Whatever you do, minimize, resize don't help. This only thing you can do is logout of that session but all the working history will be gone(of course I can save that but it's awkward)
I'm eagerly wondering is there any solutions to this? I use ctrix XenApp plugin 11.0. The other platform info:
Linux 2.6.9-67.ELsmp x86_64
OS: RedHat Enterprise Linux 4.0 U6