Driving Delta-Sigma ADC with reference clock output from MCU
You need to look at the port driving capabilities of your MPU (you didn't say which are using) and the requirements of your ADC converter. It almost seems that it's not an high impedance input but some low-impedance or current mode signal (clocks are often transmitted in this way).
Most probably your GPIO is overloaded, or it's configured in a low power mode. As for the effect on the conversion in you ADC sheet there are info on the required levels and duty cycle for correct operation.
Need more info on the MPU and ADC to say more.
What is the result after opening the trace?