Hi,
Thanks for sharing the dataset and the source code,
I found a few errors with the latest bids validation version (mostly formatting and bad json).
Here is a script with the patches to apply (already generated + scripts to generate the fixes), and a batch script that apply these patches on the data.
Issues includes the one shown in the below logs.
Only errors have been fixed (not warnings).
msc.zip
bids-validator.8779750.out.txt
Let me know if I can be of any help.