I failed to put in my original post that 50% of the substrate was taken from an existing setup that was over a year old, and it was allowed to cycle for 4 months prior to planting the shoal grass.
Here's your problem!! I know cause it happened to me too.
Your "old" substrate is full of detritus and nutrients. It should ONLY be used to top up the top 1 inch level.
Imagine. In your "old" setup, the oxygen level is properly distributed from the top to the bottom. Once you move it, all of the sand is exposed to high oxygen levels. Also, however much you clean the "old" sand, it never seem to be clean.
So, basically, if you use 50%, even just for the top, your old sand is at least 2 inches deep. At this level, before your sandbed is fully established, the detritus in the "old" sand starts to decay. The decay will quicky use up oxygen ... Thus, over few weeks, all the oxygen gets depleted, and Hydrogen Sulphite (black stuff) forms.
To avoid this in the future, do not add more than 1 inch of "old" sand to your new tank.
HTH