I've never seen that before... Curious.
If tells are going through, it's connecting. If something like Anti-Virus or Firewall was interfering, then tells wouldn't even work. My guess would be the client itself: right click on a chat window (the one with the Chat tab, for example,) and click Edit Tab. Do your channels show up in "Selected Channels"? Does moving available channels into Selected make the chat appear again?
Sometimes, my custom tabs (1 2 3 4) lose their channels and I need to reassign them from Available Channels when I edit the tab. I don't know what's causing that, but it's not happening frequently enough for me to call it a serious bug. Let me know if that's it.