Your speculation isn't far removed from mine. It's what led me to theorize that since there isn't a true "auto polling" feature similar to what the 1070 and 970 have, it would be appropriate to simply allow the 990 to ignore the very existence of the stereo analog input when a digital input is connected.
The clock's been a bit odd since a software update a while back to help deal with some spamming. I think that it has itself confused between Eastern and Greenwich time somehow.