Switching any audio signal will have an effect. On the pre/post there are crossfades on the switching, which helps, but you may still get a bump on the sound.
In general, you should try to never change routing or load presets with signal passing through a system. Any system.
That said, the "chirp" he describes suggests there may be some kind of feedback present, which is easy to get with a pre/post system. I would suggest experimenting with the wiring and the grounding – this may be a factor.
