Emailed the author and he said there's a fixed version that should be released today.

"I fixed fpse since the last update 65 of nvidia shield 2 days ago. I have to post it today."

The internal storage in /storage/sdcard0/ and the external one is /storage/sdcard1/.

Can these be set in fpse.ini?

I'm also having this same issue.

Internal storage works but not the external.

Nvidia Shield version 65.