I thought In the Hunt was fixed, but maybe not? I guess I might not have tried it, but I could have sworn I did.
The Fenrir is really picky when it comes to proper rips, and I'd advise sticking solely to Redump stuff. There are archives for those. Once I started using those, I haven't had any issues. I was actually able to fix several that were busted on the audio front, but it took a lot of manual fixing in the CUE files and whatnot, basically converting to what Redump uses, but even that isn't foolproof.
Also, if you run into a problem game (Steamgear Mash and Shining Wisdom come to mind), booting into the CD player first when launching, then running the game from there clears up the issues.
EDIT: Okay, yes, someone said on Twitter that Redump In the Hunt works on the last two firmware versions.