mattp,
HDMI_FRUN_EN did not work in Graphics mode. Although, I find that setting the VIDEO_STD to 0x3F makes the Horizontal and Vertical signals stay high and not generated a frequency. The best solution I have is to handle the IRQ from the ADV7842 and read the LCF, LCVS, and FCL values. If the values match an entry from Table 56 in the UG-214 I set the VID_STD to that resolution and if they don't match I set the VIDEO_STD to 0x3F. This way I can still continue to use my same video detection routines that work with the digital video processor.
Thank you for your help investigating the issue,
Matthew