I know it's an old part, we've been shipping these for quite some time. That's why I'd like to be able to fix units in the field via a software update! 
We already dialed the number of retries up to 15 (the highest possible) prior to asking for help, and it made no significant difference in behavior.
I notice the "Common HDMI Transmitter Applications Issues" http://ez.analog.com/docs/DOC-1429 shows a 20 KHz bit rate in their calculation for EDID read delay, but I don't know if this applies to the AD9889, one of the other chips, or if that value was pulled out of thin air (the PowerPoint didn't specify). If we could slow the EDID reads to the mentioned 20 KHz, I'm pretty sure it would fix our problems.