can you share the code with us? I have the same issue here too...I put the capacitor under test between a GPIO pin and ground. Then I put a resistor R across the capacitor.
1) Set the GPIO pin to output and send high to charge the capacitor.
2) Set the GPIO pin to input and allow the capacitor to discharge.
3) Trigger an interrupt on the falling transition.
4) Repeat the process.
5) Measure the time it takes for N such cycles to take place, using a timer module. Select N to suit the range and resolution required.
6) Convert to capacitance.
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