I set up my pedal switcher (Mastermind PBC) with a page to control one of my H9s as a looper, thus enabling my pre-post input function. I'm getting a loud pop, louder with the more gain on the preset, when switching from pre to post.
As far as I know, that is normal operation when switching pre-post. I can imagine all the relays flipping around. You have reasonably quiet switching pre-pre or post-post?
I have the same problem…to the extent that I rarely mix pre and post presets in one song.
As Mr.Camn points out, there is a lot going on when you switch from pre to post or vice-versa, so it will not be totally silent. There are fades on the changes so it should not be too noisy.
It would be interesting to know if you get the same thing with nothing plugged into the inputs - it is possible that you are feeding it DC or some steady signal. You certainly can't expect a clean changeover if you are playing at the time of the preset change.