For the benefit of anyone else stumbling upon this via Google (I understand the last post is a year old), and trying to get Retroarch to work with Parasite Eve 2 with PSX Beetle HW.
PE2 really hates having certain settings changed from defaults. The 2 main ones are;
-CPU Dynarec (disabled)
-CD Loading Speed (2x)
Here's a quick screenshot of settings that should guarantee to work (with Retroarch on Windows anyway).