Low pass filter output
I think you have two problems here:


Your choice of the OpAmp: 


The 741 is ancient and has very bad specs compared to modern parts. Most notably the input impedance is 300k worst case. That's in the same ballpark of the output impedance of your voltage divider at the negative input terminal. This, along with the input bias current will cause a huge voltage error to develop. 

The remedy: Lower R1 and R2 by a factor of 10 (or so) and adjust C1 accordingly. Or use a better opamp.


The leakage current of your capacitor:


If you've used an electrolytic capacitor for C1 there will always be some leakage current. You can think of this leakage as a resistor in parallel to C1. How high this leakage is depends on the capacitor, but it can be surprisingly low. 

Now take a look at your circuit: R2 is of a relative high value, and the output voltage is directly defined by it: What happens if you put a second (leakage simulating) resistor in parallel with it: The total resistance from output to inverting input will drop and so will the gain. You'll get a lower voltage at the output. Just as you have measured. 

Again the remedy is to change parts: Use a capacitor with a very low guaranteed leakage or use a capacitor type (film) that has negligible leakage and use a capacitance multiplier circuit to scale it up to the value you want.