The core analyzer logs for the above experiment (this time run on a different TTL channel on a different DIO-SMA v1.3m card):
Log channel: 47
DDS one-hot: True
OutputMessage(channel=15, timestamp=64833016901496, rtio_counter=64833016779352, address=0, data=1)
OutputMessage(channel=15, timestamp=64834016901496, rtio_counter=64833016796240, address=0, data=0)
OutputMessage(channel=15, timestamp=64835016901496, rtio_counter=64833016799816, address=0, data=1)
OutputMessage(channel=15, timestamp=64836016901496, rtio_counter=64833016804248, address=0, data=0)
OutputMessage(channel=15, timestamp=64837016901496, rtio_counter=64833016807176, address=0, data=1)
OutputMessage(channel=15, timestamp=64838016901496, rtio_counter=64833016810440, address=0, data=0)
OutputMessage(channel=15, timestamp=64839016901496, rtio_counter=64833016813528, address=0, data=1)
OutputMessage(channel=15, timestamp=64840016901496, rtio_counter=64833016816640, address=0, data=0)
OutputMessage(channel=15, timestamp=64841016901496, rtio_counter=64833016819648, address=0, data=1)
OutputMessage(channel=15, timestamp=64842016901496, rtio_counter=64833016823176, address=0, data=0)
StoppedMessage(rtio_counter=64836041979152)
It seems that everything is in order re the RTIO log.