I've seen the same problem, but it depends on the monitor. Some monitors are no problem, others don't want to cooperate. I also only see the problem with the carrier board included in the development kit. I happen to have a different carrier I am working on, and I have never had this problem, so the problem seems specific to the HDMI implementation on the carrier in the dev kit.... not the Joule module itself.
Fixes to try: (1) plugging in the monitor AFTER booting (2) plugging/unplugging after booting (3) running the HDMI cable through an HDMI amp or powered splitter (4) if using an HDMI monitor powered off USB, use a powered USB hub connected to the Joule rather than a separate power supply (there can be a problem with grounds not being consistent if an external power adapter is used; I don't know if this is the problem here, but I've seen it before with portable USB-powered monitors).
If (1) or (2) works for you, great! (3) costs extra but is handy when travelling and you know you will need to plug into some unknown monitor/projector for demos with limited time to sort out issues. (4) is specific to portable USB-driven monitors.