We are using an Agilent function generator (33250A) as the input. With the picoscope software, Picoscope 6, we confirmed that the signal was as we expected (540 kHz, 500 mVp).
Now, in regards to the sampling issue, we accounted for the actual sampleinterval by having the function return sampleInterval, thereby accounting for the actual sampling frequency of the scope. With this knowledge, we should be able to properly determine the sample interval and frequency content. I should say, we've repeated this exercise in Block mode (i.e. have the function return the sampleInterval), and had no difficulties properly determining the waveform frequency content.
Thanks for your help