Could you please make sure your device configured as player device?
I don’t think is that issue related to the footswitch.
If the pre-recording enabled on the device it might be the case when you trigger the playback the device has to switch from recording mode to playback mode and also have to switch the sample rate.
But to be honest I don’t see the reason to have any noise on the outputs.
Are you using the device in playlist or standard playback mode?