Yeah, a small bit of the filament tends to get stuck in the nozzle, so unless you let it push the new filament through, or do it manually whilst the head is hot and manually prime the nozzle, you'll always get that bit of leftover from the last filament.
I also get the prime circle and first layer knocks... and chalked that up to the head not being fully at temperature yet (although it seems they are no longer doing the priming circle whilst heating the head up from calibration temperature?), so I'll try lifting the offset slightly also. Although I also think the extruder is feeding a bit to fast when doing infill, as I get a small amount of knocking then during the print generally, but not when it's doing the walls or skin.
@BoozeKashi Do you happen to know of the top of your head what setting I can change for the embedded cura2 on flux studio to slow down infill extrusion a bit?