I’ve had similar problems in the past with an AIO, the pump should always be at 100%, so I usually do this through BIOS. My old Mobo had a dedicated pump pin, but the new one doesn’t, so I put it on a fan one and configured it to 100% all times. If the pump is not at maximum it might not move enough water for the system to cool.
The problem here might be a difference between how Windows and Linux handle fan control, CHA_FAN1 is a chassis fan, it might be that Kubuntu is not using the CPU temp for it, instead relying on another sensor.
Although to be honest I don’t think this might be causing your issue. I’m leaning more to thinking this is related to either the snaps or some problem with the disk you have Linux on. My recommendation is to test a live iso for different distros, if the live iso for Kubuntu works better than on the disk it might imply some issue with the disk, if it’s also slow it might be a problem with Kubuntu, I would recommend then testing different distros with KDE Plasma, they would look and feel the same but might be faster if the problem is Ubuntu’s snaps. I personally don’t like it but I’ve heard people speak highly of Fedora and OpenSuse.