As previously mentioned, you will always get a comb filter effect with almost any digital equipment if you mix equipment dry with actual dry on an external mixer. This is because processing introduces a delay, and even the A/D/A converters introduce a delay of around a millisecond.
But, if you are getting this with relay bypass, the problem is probably somewhere else. Connect the in and out cables together (which is what relay bypass does) and see if you get the same result.
