This is SO STRANGE because things have just worked up until a few weeks ago, unchanged, nothing touched. So much so that I thought, oh right, the remote's batteries must be dead. If there is any debugging info I can provide I am more than happy to, my setup:
OpenELEC 4.2.1 x86_64
Flirc 3.1 (was running on 1.0 prior)
Logitech Harmony 650
US, grounded outlets, brand new electrical actually
Remedies: moving the flirc to another USB port sometimes works, waiting sometimes works..short lived either way sadly.
Flirc is velcroed to the bottom of the TV chassis and a USB extension cable runs to the PC.
I have 3 PC's throughout the house with this setup and all 3 started having the issue at the same time.
edit=added more details