It seems obvious: when testing new firmware ALWAYS use the original remote. Using a harmony only adds another "uncertainty" in the chain. Also you can plug in a usb keyboard on your device to configure it, for example enable ssh.
I found the remote. Does nothing. Also in the Harmony I programed again minix 8X and Microsoft MCE. Nothing.
I attached a keyboard and could config the system but I need the Harmony to work.
Any other ideas?