Herratic Behavior on MCU temp

Just installed a SKR mini E3 V3 and flashed it on my modified Ender 5. Before the new MCU, I was using the built in sensor in the controller to control the mainboard fan via a TEMPERATURE_FAN but since installing the new one, I noticed some weird behavior. The temp seems to drop ~20C and behaves herraticaly and thus I cant use this sensor in the control loop. I`m trying to figure out if this is a software, config or hardware problem. Klipper and Rpi are updated.

Any help is appreciated.