Thread Crackling with 2i4, Class Compliant mode is not fixing it

I've been having a pretty irritating issue for months now which seems to be exclusive to my focusrite & Ableton 9.1 (also 9.1.2) on Mavericks where I get this wave of bizarre crackling/static sounds every 5 - 8 minutes or so. It happens when playing through my interface, so mic or guitar/bass signals and it does seem to be exclusive to Ableton, I opened Logic Pro and played for a while through that without issue. I have tried literally EVERYTHING I can think of, including sending my interface in for repair - which apparently was not the issue (they still swapped the board for me just to be safe.)

The only thing i've ever come across is the "class compliant mode" fix on the focusrite website, I installed and ran that app - it asked me to unplug the scarlett, and restart, which I did - but this problem still persists. Is there some other confirmation I should be getting that it's officially in class compliant mode?

These are a few samples from when the static has occurred in my recordings (these were the only items in the file at that time, so it was not CPU overload as it was at 4%) https://soundcloud.com/chriselsasser/crackling-problems-again-osx & https://soundcloud.com/chriselsasser/whatiscausingthissound-no-reverb

I have of course adjusted buffer, latency settings ranging from 64, up to 1024. Also plugged directly into my macbook, tried plugging in through a powered USB hub, tried removing every other peripheral from my mac so it was just the interface and my mac.

My system is a very capable Retina Macbook 15" 2.7Ghz i7, 16GB ram, Mavericks, and is not experiencing any CPU overload.

Please note this does NOT occur with my older M-audio USB interface in any software... only my 2i4. Any help is greatly appreciated, I don't want to have to move onto another brand.