Why would a current transformer act like a high pass filter, how can I estimate the low frequency cutoff?
You can arrive at an estimate by first calculating the inductance of the secondary. This may be on your data sheet, or it can be calculated from the number of turns, turn area, and core material. From there, the high pass response will depend on the input impedance to the amplifier you are using to buffer / amplify the sense signal off the secondary or the termination resistance (whichever is lower... probably the termination resistance). Specifically, it should be fl=Rterm/(2*pi*Lsecondary).