The x1 probe acts as a capacitor load on the circuit filtering out the noise. Also look carefully at your lead placement relative to other wires, are you using unshielded wires?, do you have a CCFL lamp on near the measurement point? Does changing the length of leads from the MCU pin to the scope measuring point affect this?, check the way you are grounding your oscilloscope to the the MCU board you are working with. Where are you placing your fingers...near the probe tip?