Hi Ricardo,
I have the same issue using the 4S156 atlas from AtlasPack (GitHub - PennLINC/AtlasPack: Combined cortical/subcortical atlases for xcp-d and qsiprep) and QSIPrep v0.19.1 via Singularity. The anat hsvs output and the connectivity matrix plots (that do contain the custom atlas) and FOD plots are present for the participant in the qsirecon folder, but no dwi folder. Similarly, no errors are reported by QSIPrep despite the missing output.
I originally ran this reconstruction using a pipeline configuration JSON that did not include the default QSIPrep atlases, but I think this discussion suggests that the custom atlases should be added to the atlases list as you have done in your custom mrtrix_singleshell_ss3t_ACT-hsvs.json. I am now testing whether including the default atlases in my recon spec JSON makes a difference.
I will give an update if I find a fix for this issue. Please let me know if you find a fix as well!