Can anyone here help me build a capacitor?
I suspect it is a combination of a few things:
1) The capacitance is much lower than when you are using a reference capacitor.
2) The discharge time is much shorter with your self-built capacitor
3) You are picking up 60/50Hz noise that is compromising your measurements.

Have you calculated how much capacitance you should be getting?

What value are you using when you try it with a reference capacitor?

Try shielding the system, for example putting it into a metal box. Even a grounded metal plate under the test system may help.

Why are you only using 1.5V? I would use a much higher voltage to reduce the effects of noise. What voltage does your data acquisition system tolerate?

What is the input impedance of the acquisition system.

How long does the capacitor discharge take with the reference capacitor. What is the sample rate of the acquisition system?

kevin