Can you remove the field outdir from the parameter files? I'm not sure if this is the source of the problem, but according to the parameter files, these are the same for every VOI. I suspect the field isn't being used because there looks like there is a potential bug in the code. If outdir doesn't exist, then you should get PPI folders that are labeled with the region names.

I would cd into the 1st level SPM directory before running the PPPI command. As you are overwriting files that you may be trying to read at the same time, this could be the cause.

If you run one subject at a time and one seed at a time, do you encounter the issue OR is it only when they are run at the same time? 

The only thing that I can think of is that some paths are being crossed in the configuration and PPPI line, but not in the PPPI code. If you run it outside of a try loop, do you get any error messages when moving the files from the 0001 format to the contrast name?

Can you also try this new spm_contrasts_ppi file?

If you still are having issues, can you send me your script file and I can try and replicate the issue with another dataset.