We figured it out - looks like only plugins with 3 letter extensions get pulled down. My coworker copied one of the .exe files in the Windows plugin folder (on the XI server), and renamed it. After configuring a new NRDS test with the new executable, it successfully pulled the file down. We then tried a .txt file, and a .prl file, and both of those work, while .pl files still don't work.
We looked at the NRDS_Win.vbs code (R3 version) and it looks like the problem is the regex around line 483:
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file_name.pattern = "\$PLUGIN_DIR\$\\([^\\/:\*\?""<>\|]+\.[\w]{3})"
It may be good to do 3 letter extensions, but also allow the common scripting languages like pl, py, etc...
Thanks for your time and effort helping us - and best of luck with NRDS going forward - it seems very promising, and I'm sure it will only get better with time.