Switched capacitor circuit
When I do a probe of the voltage with a scope across C1 the voltage
read out is 5v instantly

That might be a problem if you are using an earthed scope and your signal generator is also earthed on its return wire. Instead, try probing the drain of Q1 and the top of C1 with two probes and subtract the voltages.
$$\boxed{\text{OR}}$$
C1 could charge instantly (well not really instantly, read-on...) because of leakage current in Q1. It might take a few hundred milliseconds or even a few seconds but, by the time you come to check it out, it will have charged and the show is over so to speak.
$$I = C\cdot \dfrac{dv}{dt}\longrightarrow dt = \dfrac{C\cdot dv}{I}$$
So, if C = 1 uF and \$I_{LEAKAGE}\$ = 1 uA then it'll charge to about 5 volts in 5 seconds.