If you must feed both channels the same source for some reason, try a distribution box instead of a Y cable. Something like this may be what the Dr. ordered. http://www.sweetwater.com/store/detail/ProD2/ Most shops that sell electrical instruments will carry them.
We had this problem when we first got our scarlet but the firmware seemed to fix it. Are you running the mics directly into the inputs or routing them through a mixer first? For some reason when the signal is coming in post mixer, there is no interference. Also, taking our camera off a surge protected outlet seemed to fix it as well.
Try booting the camera up without a lens attached, attach audio, then lens, and see if that works. Try removing and reinstalling the mount to remove any electrostatic buildup. Contact the 24/7 Support line, they'll probably have better advice than me.
try using a ground lift (2-3 prong adapter).. this will only help if your problem is a ground loop.
Otherwise if nothing else is helping you... cheapest solution will be a tascam DR -05 and a Rode condenser shotgun with a battery to record your primary audio.. use the headphone out to feed reference audio to your camera... this should cost about $400-$500.. and you will be able to sell the combo for $300 or a little more when you are done.
People having problems - are you sure your audio cables are wired correctly? Mini-jacks being used as balanced audio inputs are not an industry standard.
I need to run a new test feeding from a mixer vs mic patched directly to camera and phantom powered by camera. I haven't run mixer audio to camera since most recent firmware update, only mic direct to camera.
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