Rarefaction.shared still with issues

Regarding the rarefaction.shared command, It appears that we still have an issue (I have reported a related issue before, (Issues regarding Indicator, chimera.vsearch and rarefaction.shared · Issue #729 · mothur/mothur · GitHub).
I am running this data again (it is part of a course I teach in the university), and the output is not correct.
My dataset has 3 treatments (Y, N and O), each one with 5 samples. Mothur recognize all three, but the output file put every sample with the same name (only Y).
Additionally, it calculates values for only four samples per treatment, instead of 5.

Warm regards and thanks a lot for your work in improving Mothur!