crackles and distortion

I recently purchased BAL after using the demo version for quite some time, I have begun get a large amount of crackling and distortion in my sound when i use the BAL pipeline but everything is crystal clear when i make my usb interface the main output source.

I have tried the following solutions based on a quick google search of previous posts form this forum and several others.

1. Edit the ini file to include Startup Delay=x
2. not running BAL on startup
3.changing sample rates to 44100

any other ideas would be very helpful. I have been having this problem for ab out 2 weeks now but it always seemed to resolve itself but now its very persistent and annoying.

Here is a list of specs to save time

Corsair Graphite Series Black 730T Full Tower Case
MSI X99S SLI PLUS ATX DDR4 NA
Intel Core i7-5930K Haswell-E 6-Core
G.SKILL Ripjaws 4 series 32GB DDR4
ASUS GTX980 GPU
Corsair Hydro Series H110 Liquid cooler
Toshiba 3.5-Inch 2TB 7200 RPM HDD
Corsair AX860i Modular 80 PLUS Platinum PSU
2x SanDisk Ultra II 240GB
Monitors: 3 27" BenQ GW2760S

Recording Equipment

AVerMedia ExtremeCap U3 capture card
Panlong 2-Port HDMI 1×2 Powered 3D Amplifier
Alto ZMX122fx Mixing desk
Focusrite Scarlett 2i2 USB interface
Audio Technica AT2050 Mic
2x 3.5mm to Dual 1/4" jacks TRS cables
Logitech C930e webcam