Should SMB capacitors read their values after soldering onto a board?
Apparently the specific board network of connections interferes with your method of measuring the capacitance. The caps are apparently connected differently. The usual method employed in DMMs for measuring capacitance is to charge caps with short pulses and measure RC reaction to this. Or measure a frequency of some internal generator with the cap under test. If your top cap has a parallel connection to a small resistor, the DMM will have false readings.

In general, there is no reason to check "capacitance" on soldered components, since they might be likely a part of a complex network and can't be characterized by a single "capacitance" parameter.