I have the .pl extension registered, and the command I was trying to execute via open3 was simply "stats.pl". Even though Windows was searching the path and finding it successfully, File::which will not find it, so I had to write my own variation. I first fully qualified the program name, and then determining that it was a perl script, I preceded it with an explicit call to perl. Then open3 did not need to run it in the command processor and I was able to make a full run without failures.
I'll continue to complain in the windows forums about the command processor failures.