Reviewing the EPIA-EN motherboard User's Guide, I found a PANEL jumper block to select the following:
TVD4/DVPOD4 – AGP Port Muxing (ON: 2 12-bit DVI interface, OFF: 1 24-bit Panel interface)
TVD5/DVPOD5 – Dedicated DVI Port Configuration (ON: TMDS Encoder, OFF: TV Encoder)
I thought I had checked all of the jumpers long ago. How did I miss this jumper block? Well, it was
NOT populated on my board!

I tried using some tweezers to short the connection but I'm not sure if it is horizontal or vertical. The photo of the board indicates horizontal but the document suggests vertical.
LinITX has a photo of the EPIA-EN 15000 without the PANEL jumper block. Perhaps it was lost in an update of the PCB?
http://www2.multithread.co.uk/mtcsho...board_main.jpg
I'll look for updated docs. I need to get some rest and resume debugging tomorrow.