Audio drops and causes loud pop when using JKL in prelude CC 3.1.0 (128)?

I'm using a mac pro 2010, osx 10.9.5 with firewire audio through mackie onyx 1220i. I'm logging footage off a usb3 external (at usb2 speed since I dont have usb3 on my mac pro 2010), The audio will consistently drop out when using JKL scrub (particularly back scrub with J)  and when it comes back it cause a loud pop, the kind that makes you worried your speakers are going to blow, like when you turn off a synth at full volume before turning it down on the mixer. Super worried about this issue and Prelude possibly blowing my speakers. Seems like a bug?