Hi Ash,
We found several instances of incorrect termination of the related pins in the document you linked to. After correcting these, the severity of the issue may have been marginally reduced but it is not eliminated completely.
We have been trying different configuration settings and different configuration devices with no luck. The longer the board is powered, the worse this issue gets. Not only does the issue happen more frequently over time, but the amount of time it spends trying to configure increases as well.
The duration of the time spent trying to config is also very random. Ranging from 1 to 40 seconds.
Do you happen to have any more insights or data points we could get?
Thanks