You're creating a high pass filter between your capacitor and whatever resistance you're connecting to Vref with. In the first circuit, I can't see the impedance to Vref, but it's apparently not zero. In the second circuit, it's the output impedance of U_2; again, it's unknown to me. I might be able to estimate them if I knew the frequency of your test signal.
In the 3rd circuit, the 10K with the 0.1uF gives you a corner of about 159Hz; using the 330K brings the corner down to about 5Hz. This leads me to suspect your signal is in the 50-80Hz range.
The 4th circuit pits your 0.1uF against a 50K load, giving you a corner of about 32Hz. Changing to 680K resistors brings the load up to 340K (they're effectively in parallel from a loading standpoint) and again close to 5Hz corner.
You need to pick your R and C so that the lowest frequency of interest is higher than the 3dB point of the filter; you might want to make it about 3-5 times higher if you're trying to minimize distortion.