OKAY I FIXED IT
This is for the VIA EPIA-M920-16QE
The power button headers are Pins 6 and 8 which you can see under section 2.2.6. Front Panel Pin Header
http://cdn.viaembedded.com/products/docs/epia-m920/user_manual/UM_EPIA-M920_v2.07_180321.pdf
These are listed as
6 PWR_BTN
8 GND
From the Flirc SE manual, pg 5, the diagram for the Power SW cable from the Flirc SE to the motherboard does not clearly state that the polarity must be followed through and the motherboard doesn't label it clearly as well
http://www.streacom.com/downloads/ug/flirc-se.pdf
All it took was to switch the polarity by flipping the header around.
Guys at Flirc, could your diagram be clearer? The non electrically inclined person wouldn't know that the polarity was an issue. After all, just closing the gap between the headers is enough to boot the machine.