Take the Continous Cotton example and add to the outputfile variables (output daily) -
You will see that at harvest, the cotton trash is added to surfaceOM_wt but does not appear in the cotton pool (surfaceOM_wt_cotton).
Note that the crop_type is reported with a capital C even though the ozcot.xml has lower case.
Some experimenting with maize worked as it should and the crop_type had a lower case m.
If the SurfaceOrganicMatter component is initialised with a Pool name with Cotton (capital C) then surfaceOM_wt_cotton is unknown for reporting.
It looks like the pool name is case sensitive and the cotton trash is going into a pool called Cotton which cannot be reported due to case.