Greetings,
I just went through setting up a Yubikey NEO with pass.
I got all the keys exported properly, and went and re-encrypted all my entries with the new subkey. The Yubikey is successfully working on the CLI and also on android-password-store on my phone with Openkeychain.
When I try to open a password entry in qtpass now I see the following:

Let me know if there's anything else I can provide to help diagnose.