The nature of your setup is unclear to me. But, judging from the symptoms, I'm guessing that you are using send and return to the TF, with an analog wet/dry mix.
This almost never works with digital equipment – due to the processing delay, if there is any dry content in the output you will get some phasing or "comb-filtering."
It's not just an issue with our products. You would do better to use the wet/dry mix in the TF.