So I disabled it, and played a few rounds of SNK vs Capcom 2, and some time around the hanger in Tony Hawk 2, and it works perfectly! Thanks! :D

@pjft said in Random 1 second freezes with all PSX games:

@njscorpio turn it off. See if it helps.

Pi Model or other hardware: 3
Power Supply used: CanaKit 2.5A Micro USB Power Supply with Noise Filter
RetroPie Version Used 4.2
Built From: Flashed retropie to work through Jessie, made a disc image copy to place onto new (not working) micro sd
USB Devices connected: keyboard, ps3 controller (via bluetooth)
Controller used: ps3
Error messages received: none - system stops during boot
Log found in /dev/shm/runcommand.log (if relevant):
Guide used: youtube install instructions
File:
Emulator:
Attachment of config files:
How to replicate the problem: plug in retropie to turn it on. system stops during boot process.

So, after some testing and reading, I guess the problem is the SD card speed. Although mine is a SanDisk Ultra 64 GB Class 10 I had to overclock the card reader. This thread helped me. Anyways, I might also try loading through a external drive.