Hi Andy,
The AD8302 is not a lock-in amp, or at the very least, it is best not to think of it as such. The phase detector is an XOR style that basically detects the zero crossings of the limited outputs of the log amps (page 15, last paragraph on the left). The phase detector output is then averaged to a DC value, which is essentially VPHS. As you mentioned above, sometimes the averaging isn't enough (this depends on your input frequency) and you must put an external filter cap on the PFLT pin.
Thanks,
Joel